I have similar issues of 100% usage causing multi-tasking issues, itunes to sound like a bad DJ, to occur system wide. Very out of my mojo flow stuff.
The solution I could find was to limit the CPU cores affinity can use to 75% of available CPU power and my issues are now resolved.
This is done on Windows by:
Task Manager > Details > Right Click Designer(or Photo/Publisher).exe > Set Affinity > Uncheck Desired Cores
Serif Affinity Suite is amazing, yes there are features that are not yet made, but for a single-purchase software (Thank GOD!), it is to the moon awesome value and performance that is really just remarkable. Publisher is a dream come true with the personas... anyway nuff my promotion, hope this helps.