I had a similar issue with my older Focusrite Saffire Pro 26 I/O. I updated to the latest focusrite "control pro" program and through that was able to update the firmware on the Saffire Pro 26 unit.  After that the problem went away.  
 
For the 40 Pro, I think they call the program Mix Control.  
 

 
 

Hughkills: As far as I know, everything is all up to date but, I will check.

Hughkills: Yes, my Focusrite Mix Control is up to date.

all good ideas here,
 
I would check the bios and make sure it set as hi as possible and if it was set to full turbo or over clocking, it may have reset back to default. it happens.
 
Another thing I discovered by accident that seems to have fixed some Splat running issues.
if you have been trying different audio drivers with no luck. as I was.
so, Each time I change the Audio drivers now, I "reset to default" from within the configuration File menu option.
I have now done this on all of my systems running deferent audio devices and they are all running smother.
 
I have not spent much time on this but it looks like the Configuration File adapts to the selected drivers.
Maybe a glitch on something that is suppose to automatically change ?