twaddle
 

9) Update your motherboard chipset (try Intel driver update site) and BIOS

 
Always a bit scared of doing that, p[artly because this is an overclocked machine that was built by a bespoke audio company and I'm concerned that updating bois will over ride those settings that I have no idea how to configure manually.

This is important, and one of the likeliest causes of your problems.  Many motherboards allow the user to backup your current BIOS settings in case you need to restore them later.  Call your DAW builder and have them guide you through it if possible.   Either way, what's more important to you, having an OC'ed machine that's giving you grief, or a non OC'ed machine that's working great?  I would worry more about getting this issue fixed, then later, you can see to OC'ing it again.
 
Also, don't assume that because you've upgraded to Win 10 and have all the updates, that you're good to go.  Odd as it may seem, sometimes you need to go to Intel or your graphics card manufacturer, etc. to get their latest drivers.  I would absolutely check your Intel chipset and your video drivers to make sure they are the latest.

twaddle
Well, I've just unplugged everything from my USB3 sockets and plugged them all into the boards USB2 ones.

You don't need to move everything to a USB2 port - just your audio interface.  And try to have it on its own bus/controller.   By putting everything on the USB2 ports, that could create yet another problem with too many things fighting for bandwidth.  
 
I've always used a dedicated USB or Firewire PCI(e) card just for my audio interface, and have never had these kinds of issues.  The cards are relatively inexpensive and worth looking into if you're still having problems after trying all of the other troubleshooting steps.  Good luck.

A couple of further suggestions.

Make sure cpu core parking is switched off (registry setting, google will find it for you).

Disable the E(whatever) cpu sleep states in BIOS.

Both the above result in Windows either slowing the cpu down or in the case of core parking shutting down cores and switching the load to fewer, more heavily loaded, cores then switching cores back on when the active ones run out of steam. Neither are noticable using the office applications, photo processing or even gaming, but can mess up real-time audio or video processing very badly.

Windows was never designed with real-time processing of anything in mind and these power-saving "features" don't help in the slightest.

The DPC Latency Checker is invalid for Win 8/8.1/10.  They have a note on their web site and for the last couple of years say they are working on an update but they have never produced it.
 
 

fireberd
The DPC Latency Checker is invalid for Win 8/8.1/10.  They have a note on their web site and for the last couple of years say they are working on an update but they have never produced it.

Latencymon is better anyway...

Latencymon is better, but it can "overload" you with data and sometimes hard to digest it all.

fireberd
Latencymon is better, but it can "overload" you with data and sometimes hard to digest it all.

Not really, just go to the drivers tab, sort it in order of dpc and Bob is your uncle. That's the data you need (something the other util isn't very good at). Unfortunately you do need to digest that info if you need to get to the heart of the matter... not much choice..

Whatever is causing this noise latencymonitor isn't reporting any issues I'm afraid.
 
Steve

Oh wow. I just listened to your sample, Steve. How horrible! You have my utmost sympathy.
 
This probably isn't a DPC latency or USB issue. I would have suspected the audio interface, but you've already eliminated that possibility when you experienced the same problem with two interfaces.
 
If it is a hardware problem (not my first guess, though) then there's an outside chance that your CPU is overheating and dropping the clock speed in self-defense. It wouldn't hurt to open the case and give it a thorough cleaning, especially the CPU heatsink and fan (you may have to un-snap the fan from the heatsink), as well as the power supply fan. If you've never done that before you'll be shocked at how much dust can accumulate in there, especially if the computer's sitting on the floor. It's not unusual for the gaps between the heatsink fins to become completely stuffed with dust, cutting its efficiency in half.
 
I assume you already have the motherboard's integrated audio disabled. If not, that's worth a try. It sounds like you're already using your Focusrite for YouTube and movies and such, so you don't need it to be enabled anyway.
 
More likely, this is going to turn out to be a software problem, perhaps a background process or even malware. First, get a copy of Process Explorer if you don't already have it (even if you do have it, it was updated earlier this year so you might want to grab a fresh copy). Run it when everything's going smoothly to make a list of what's normally going on. Procexp has an export feature (Ctl-A) that lets you save all the details into a text file.
 
When the problem next shows itself, run Process Explorer again and export the data so that you can do a detailed comparison between the OK state and the Not-OK state. Look for processes that are consuming a lot of memory or CPU, and process that weren't running when all was working well.
 

Here's the link to Process Explorer: https://technet.microsoft.com/en-us/sysinternals/bb896653