SOLVED. I hope this helps someone else avoid going through this process in the future. Here's what I did: Compiled custom 2.6.35.7 kernel with -ck1 patchset including BFS scheduler to replace CFS. Configuration changes: enabled PREEMPT, upped polling from 100Hz to 1000Hz, disabled dynamic ticks Not only is the stuttering problem solved, but I feel like I have a completely different desktop. Everything is much snappier - much quicker than Windows. After setting the SCHED_IDLEPRIO flag on F@H, it is completely unnoticeable no matter what else I run. This is how a desktop should be. The only downside is that the system uses about 20% more power at idle (without CnQ + C1E). However, since I fold 24/7, it's never idle anyway.
