I have Folding@Home running in the background at full power (from a choice of light|medium|full), which causes no issues nor slowdown whatsoever in user interaction in all apps, including CPU intensive ones like browsers or Photoshop, except for Sublime Text (CPU intensive processes are of course affected by Folding@Home and take longer to finish, but not user interaction). Sublime slows to a crawl. The cursor moves around 1 or 2 seconds per character; typing is equally slow; the GoTo Anything menu is even slower.
This thread claims the issue is when Folding@Home uses the GPU, but in my case it runs on the CPU. Reducing Folding@Home power intensity somewhat soothes the effect, but Sublime still feels slow with it at light power.
Again, this only happens with Sublime. Only quitting Folding@Home entirely brings Sublime back to an usable level.