First time i've had this... random clicks and pops in the rendered file.

I thought maybe I had some pops in some sound splices of samples... maybe i forgot to shorten and fade them... but when i zoomed in and listened in different players, the clicks are in different places... WTF????  No clipping or funny peaks that I could see.
anyone ever see that before?

but it's in the rendered .wav, flac, mp3 playback in different places??? played back in audacity, WMP, whatever... the noise is still not in the same place on the recording.  must be halloween.

The Interweb is the main culprit for me.  Most of the time it doesn't cause problems but pops and clicks always seem to happen during a great take  so I turn it off most of the time. 

I have seen this before and in my case was introduced by Windows processes with higher priority. The wi-fi driver is a huge offender, but there are others. Take a good look at processes running and disable (esp at start up) ones that you do not need.

I think something to do with the audio drivers and cpu or other gear or MB issues might be at hand in this one.
 
Random clicks and pops...is a sure sign of something not working right..or conflicting with...((as I see it))
 
So try some tweaking of the system..if not already done...a wide list of things to do....if you seek em you will find em here, already posted of past troubleshooting methods...and setup for...Audio, with Firewire and or USB or thunderbolt or ethernet...ect...
 
So you can also try buffers and such...but that is not going to solve for random noise...The cpu, memory, or other IRQ interupts will cause on random timings of the system...and or apps running in the background....which can cause interupts of playback, and or video playback.
 
""Turn off redundant devices "" = /no overclocking/speed step and VT/wi fi/ internet nic, and or on board audio if not needed...and no HDMI audio...if not needed...disabled...in bios is one thing I do for on board gear not necessary for audio or video work....wich reduces services loaded at boot up, and driver loading...and cpu calls for them.
 
then apps running in background...redundant to the work being done, snuffed out and or turned off.
 
config sys...stop all auto updates!!...dependent on your needs also....no nic...no updates...no need for auto updates...so turn off the service would end that service from running...or booting with windows.
 
Adobe pdf reader seems to not obey here to that process.....But, it has not killed my audio...and i can uninstall now open office opens pdf files...so ways around that can be undertaken....and turn off defender, and anti virus apps.
 
Should help...?
 
if not, perhaps something with slot placement in the pc/MB and conflicts in that shared process.
setup....read the MB manual for shared slots...move any card on shared slot for audio onto one that has the least shared devices...or one free slot not shared.
 
 
Cheers.
Hope it helps..

This is from the Focusrite people:
Optimising your PC for audio on Windows 10Optimising your PC for audio on Windows 10
All of the tuning tips below should be implemented if you want to achieve high speed, low latency audio recording and playback without glitches with your audio interface. If you are experiencing pops/clicks when recording or playing back audio please try following the instructions below. Please note that the steps below assume that you have the view in Control Panel set to 'Small/Large Icons' rather than 'Categories'.
General optimisation:
1. Set your computer's power for high performance
If your computer is set to conserve energy, the CPU may not be running at full speed all of the time. This can have a detrimental effect on your computer's audio performance. To set your computer's power for high performance:
- Go to: Control Panel>Power Options
- Choose "High Performance"
- Then click the "Change plan settings" button. Make sure both power options are set to "Never".
2. Disable system sounds
System sounds can interrupt audio. Ensure that they are disabled by doing the following:
- Go to control panel and select "Sound"
- Go to the sounds tab
- Under sounds scheme, select "No sounds"
- Click "Apply" then, "OK"
3. Set processor scheduling to "Background services"
This will improve the performance of your audio drivers on your computer. To do this:
- In control panel select "system"
- Go to "Advanced system settings" and then the "Advanced" tab
- Click on "Settings.." under Performance to bring up the "Performance Options" window.
- Go to the "Advanced" tab and set processor scheduling as "Background Services"
- Click "Apply" then "OK"
4. Disable Windows Firewall, anti-virus and spyware software
These should all be disabled to ensure that no interferences occur during audio recording or playback and to ensure that maximum resources are available. To remain secure while your firewall and antivirus disabled, it is advisable to temporarily disconnect from any internet connections when working with audio. This will also make sure that no network adapters are conflicting with any audio. 
Advanced optimisation:
If you wish to optimise your system further, or you are using a system that is particularly lacking in resources you can follow the tips below for advanced optimisation. 
Disable Visual effects
The visual features in Windows 10 can use resources that could otherwise help to improve audio performance. As a start, it is good idea to disable some of the visual features by doing the following:
- Bring back up the "Performance Options" window by following step 3 above and clicking on the "Visual Effects" tab and selecting "custom".
- Untick: "Animate windows when minimising and maximising" to help prevent glitches when minimising and maximising. You can also experiment with disabling other visual effects in the custom list to see how they improve audio performance. 
- Once finished, press "OK"
If you wish to optimise your Windows 10 graphics for the best performance use the "Adjust for best performance" option.
Disable Network cards
Sometimes, network card drivers can cause problems with audio. A good troubleshooting step is to try disabling your network adapters in Device Manager, and then test local audio (like an .mp3) and see if you continue to have issues. This is also a good optimisation step in general. Disabled adpaters can easily be re-enabled at any point.
Disable Windows services
One way in which you can make more resources available to improve audio performance, is to disable unnecessary Windows 10 services as these use valuable resources. The following site has a comprehensive guide to the services running on Windows 10 and helps locate the services that are safe to disable: Windows 10 Service Configurations by Black Viper
Please note that we would recommend that disabling Windows services should be done only by advanced users.
If you are still experiencing audio performance problems after optimising your computer for audio, please Contact Technical Support

OK I have a saffire pro 40.

Sometimes this clears it up..

Uninstall mix control, reboot, install mix control (latest), reboot, reset settings and default hardware in mix control. Set it up again. It do something similar with whatever interface you have. Make sure in the end you are on latest drivers and firmware.

Other stuff.

Update BIOS and motherboard chipset drivers.

Disable unnecessary startup programs and services. Uninstall unnecessary applications from windows.

Rule out a dodgy plugin by starting Sonar in safe mode.

Download a copy of latencymon. Work it out from there.

In some cases you may need to disable network card whilst recording.

For my scenario I found Sonar JP to be the lead suspect as there is a bug that maxes out the first CPU core (check task manager). Rolled back .

It happens but it's extremely rare these situations are down to hardware (drivers and firmware maybe). If it was working before an update almost zero chance.

Cheers..

Kylotan
One unlikely thing, but worth mentioning - utilities like F.lux which dim your monitor after sunset are also likely to introduce pops into audio playback, because they make regular requests of the graphics driver that can interfere with other high-priority background processes like audio handling.

There's a setting on f.lux that stops that.

Maarkr
3. Set processor scheduling to "Background services"
This will improve the performance of your audio drivers on your computer.

 
This is along-ago debunked "optimization". Don't do it.  Drivers are drivers, not services. You'll just be taking priority away from SONAR which is precisely not what you want to do.
 

Disable Visual effects

 
Be careful with this one as well. SONAR's Now time cursor, and possibly other graphical elements depend on some of these functions.
 
I second the Doktor's order to use LatencyMon to check your DPC latency. DPC spikes are highly likely to be causing the real-time audio glitches, and LatencyMon will help you identify the root cause.
 
It's very unusual for that to manifest in files rendered offline; you might just be hearing new real-time pops/clicks on playback of those files unless they're occurring at the exact same place every time and can be seen as discontinuities in the displayed waveform when you zoom in.
 
 

Doktor Avalanche

Kylotan
One unlikely thing, but worth mentioning - utilities like F.lux which dim your monitor after sunset are also likely to introduce pops into audio playback, because they make regular requests of the graphics driver that can interfere with other high-priority background processes like audio handling.

There's a setting on f.lux that stops that.

Such as? They don't mention that in the docs, but instead suggest a video card driver update will fix it (which it doesn't, at least not for AMD cards).

Doktor Avalanche

Do NOT disable your firewall unless you are crazy.

Generally good advice, but in this situation and in the context of other things they have said, particularly disabling network/network cards, I can't see an issue, but whatever, my firewalls are turned off permanently except for in the router itself.