Agree with Jim, if the noise is increasing when you add the case, then there is probably some kind of sympathetic resonance happening. i.e. The case is amplifying whatever is causing the initial vibration.
Swapping out fans for different types/sizes/rotation speeds will help if it's a fan. Moving HDD's to a different mount will help if it's those that are causing the initial vibration. Placing a sound absorber between the computer and your recording position may also reduce the noise to an acceptable level.
Removing the case during recording would be a quick and dirty solution till you find out what's really going on.
Let us know what you end up doing as this is an issue for many home recordists and all efforts to reduce this kind of problem is always of interest.
Good luck.

Yeah I think you guys are onto something here.
 
I ran a good long session last night with the covers off and the computer sat on a chair next to me.
Yes I could hear the fans but the noise was at such a low level that one would assume putting the covers off would kill it completely.
That clearly isn't happening so there's probably some sort of acoustic bounce around happening, but it's still odd that with the pc coverdd and in the rack, the noise only build up after an hour or so of use.
 
My SPL meter only goes down to 50dB so I'll download the app mentioned by mettelus and try again.
 
There are only 2 fans inside the case - 1 for the CPU and 1 for the PSU. See picture
 

 

If I am reading you correctly, the noise diminished or disappeared when the case was removed. If so, then it is not so much an issue with the noise source as with the enclosure.

 
This seems to be where we're headed.
 

if removing the case also removes the fans, then the issue is less clear, and if it also involves removing the unit from the rack, then rack vibration is still in the differential

 
As you can see, no fans are removed when taking the covers off.
 
The next thing to try (apart from a more sensitive SPL meter/app) is to put it back in the rack without the covers. This should help to narrow down the source
 
 
Thanks guys, we'll get there!!

The two things that look like fans at the top of the picture, are they not fans, but where case fans would fit?
 
If you have no case fans, I would suggest to fit some.  They're important to ensure good airflow within the case whilst the case is fitted.  I think you have a lack of airflow inside the case when it is fitted and temperature (and hence CPU fan speed) is building up over time.
 
[edit] If that's the OEM CPU fan, ditch it and fit a quiet one.  Also, a 500W PSU is perhaps a bit on the low side for the machine spec in your signature (assuming that spec is for the machine under discussion).

+1 to adding case fans, since they drastically improve heat transfer out of the box.

I am not sure if that cheapo foam weatherstripping will compress enough to isolate the case edge from the cover and still let you get screws in, but something similar would also mitigate the cover transferring vibration to the case. Wait on that idea till you better understand the source though.

FYI, the app I used was "Sound Meter" by Smart Tools, Co. I should have mentioned that earlier, sorry.

Running the computer with skins off can be risky because it can actually lead to overheating (as non-intuitive as that seems) by defeating the internal airflow design. (I say this even though my own machine has had its side panels off since day one.)
 
I once studied this phenomenon by monitoring heat sensors at critical points with skins off and on. This was in a server room where noise was not an issue but heat was. The machines ran cooler with fewer airflow paths, because the air could be directed over the heat-producing components rather than being dispersed.
 
The easiest solution, I think, is quieter replacement fans. They're relatively inexpensive ($20-30) and fit right into the space the old fans occupied.
 
 
 
 

The size of the internal case fans is important.  Smaller fans spin faster and hence make more noise.  One of my computers started to get quite loud.  I removed the smaller case fans and replaced them with larger bladed ones. (yes I had to modify the case a little with the mounting holes) Now they are super quiet and move more air in the process and spin slower.
 
Also nothing beats putting the computer inside a rack that has a door on the front.  I have had a smallish rack case now for years that just fits two computers inside and sits under my main table.  There is a front steel door with a large dark perspex window and the whole door seals tight and literally shuts in all the sound.  There is a rear door with mine too but I have it open slightly.  The cabinte is also well vented too at the top and the bottom of the sides.  It is under a table and you don't hear any sound coming from the back of it.  I also lined mine with acoustic foam on all surfaces except the bottom surface.  Foam about 1" thick that has smaller wedge shapes on it.  This quietens things down a bit as well.
 
With the front door closed I hear nothing at all.  I can record close to it and still not hear it.  Once you experience this as they say you will never go back.  For me the sealed rack case is the only way really.  Sure you have to open it to burn a CD etc but it is no big deal.  The benefits far outweigh any problems.
 
I picked up mine in a second hand office furniture type place. I see Bristol you are running a rack mounted computer but in a way they can be noisier. Simply by the fact they are higher up and you are closer to their front panel. I have got one or two rack samplers that have even quiet fans on the rear panel but they are audible because they are rack mounted. You could still put a rack mounted computer into an even smaller server cabinet with a smaller door on the front perhaps. Its positioning may require you to rethink some of your cables and connections though.
 
This type of thing:
 
http://www.ebay.com.au/itm/6U-6RU-19-19-Inch-Network-Wall-Mount-Server-Data-Rack-Cabinet-450mm-Deep-/221942882487?hash=item33acd3a0b7:g:~BMAAOSwJkJWjGDi
 
 

Is that picture of the open case looking down on it as it is in the rack or sideways on? In other words, is the cpu cooler fan horizontal or vertical when it's in the rack? I'm just trying to get a mental picture of where the hot air naturally wants to go.

My gut thought is that a big, slow fan pushing air into the case might be helpful, so long as it's in the right place if it allows the cpu fan to be slower and prevents the psu fan kicking in. A similar cpu fan might help, depending on how noisy the one fitted at the moment is. Trouble is, not all fans and hardware advertised as "quiet" actually is, it's just a bit quieter than the small Intel and similar OEM fans that sound like vacuum cleaners when their speed ramps up. Gigabyte used to use a tiny fixed-speed fan on the m/b North Bridge chip which could be heard a few yards away.

The two HDD silencers look very much like ones I've used in the past. I found them a help with some HDD noise but not particularly effective at silencing seek noise and clicks or preventing a slow build up of initially low volume resonances from the motors that eventually could get quite noticeable. The most effective solution I found was to decouple the drives from the case by mount the boxes very loosely, either suspended by silicon bands with no screws directly linking them to the drive bay or placed on acoustic foam in the bottom of the case.

Another possibility for case resonance creation might be the fans creating beats between themselves which get magnified as they reinforce the resonance over time in a feedback loop. I had a problem last year when after an hour or two of running I'd start to get a regular slowly building "buzz.......buzz......buzz......buzz....." which was quite noticable in the room below the PC via the floorboards. The case side (a well-padded Fractal Design) could be felt vibrating.

The source turned out to be the case fan's bearing going a little rough and noisy (a long screwdriver makes an excellent stethoscope for isolating noise as any good mechanic will tell you, just keep hair, jewelry, sleeves etc. away from anything going round). The noise was so little at first I decided it couldn't be the cause of the problem, so ignored it and spent hours trying to isolate the source of the noise until in desperation I tried swapping the fan out, which cured the buzz immediately.

Poor fan mountings transmitting fan vibrations into the case or something connected to the case might be another thing to look at.

Further update.
 
I reinstalled the computer in the rack, minus the cover, ran it for a few hours and noise levels were absolutely minimal, so it's nothing to do with the rack, but definitely something to do with the case and/or other resonances echoing around once the cover is in place.
 
@tlw - that shot is looking downwards and the back of the pc is at the top of the picture, so the cpu fan sits horizontally within the case.
 
Interesting thoughts about the lack of case fans (only in this industry could a solution to noise be to add more fans heh he)
 
@mettelus - thanks for the, downloaded & installed on my phone
 
@jeff - it should be perfectly possible to fit a door on the front of the rack so if no other solution presents itself I'll have a look at making one
 

Another possibility for case resonance creation might be the fans creating beats between themselves which get magnified as they reinforce the resonance over time in a feedback loop

 
This has got me thinking.
 
Time to get the stethoscope out to try and identify which fan, or both, are causing the issue.
 
One other option would be to replace the exiting psu for a fanless model. These aren't cheap (what is with this hobby?)
 
More musings please and thanks to all.

Not sure how well a fanless psu would handle that psu position. They usually have most vents in the top to let the rising hot air out. I'm using a Seasonic 460W one which handles the sig PC's requirements OK. It hase vents in the back (where the mains cable fits) and the top is a grille. It sits at the bottom rear of the case with the case fan extracting at the top rear.

A fanless psu also makes a case fan pretty indispensable I would think. One way or another adequate cool air has to be encouraged into the case or the hot air sucked out or allowed to escape.

+1 to this. Bear in mind that heat transfer is proportional to flow rate of the coolant over the surface. The "cooling fin" design of fanless gear is pretty reliant on external airflow being provided (or open to the general atmosphere like air-cooled motorcycles, or when you pulled the cover off). As soon as a cover is installed, air is trapped except for where it leaks out and the PSU/CPU fans are then acting more like a blender - just making the inside of the box "hot" and the air slowly seeping out the ports. Case fans are ideal to pull hot air from the CPU and get it into the room and allow cooler room air to flow in.
 
A utility to monitor your motherboard (temps, fan speeds, etc.) would be recommended. If this noise occurs over time, it is highly likely the blender phenomenon is occurring (and you can simply put your hand on the case to tell if it is hot or not). TBH, I would be less concerned of noise over CPU heat, and I worry the CPU/PSU fans are ramping up speed to stay cool creating the noise you are hearing. Again, a utility to check these will let you know better.
 
A case fan will not run at high speed if the system is running cool. Other options are to leave the cover off, put holes into the upper portion of the lid (to enhance natural convection), or mount the system so it has holes as the bottom and top (and will function naturally like a chimney). I honestly would go the case fan route first and foremost though.