Well, I don't run my Folding@Home as a different user (actually, I ran it as root, though I suppose I should change that now), and I have noticed the issue still applies even to other non distributed-computing cpu loads:
"I tried to reproduce this using a simple busy loop in bash, and with 'yes', and by using cat /dev/zero or cat /dev/urandom > /dev/null, each niced to +19 and SCHED_IDLEPRIO, but for some reason, these did not create the same sluggishness that folding@home creates. In addition, these loads did not show up as 'nice' in my Gnome system monitor panel applet; Instead, these processes showed up as 'system' load, and they also sped up my CPU despite cpufreq being set to ignore 'nice' loads."
Well, I don't run my Folding@Home as a different user (actually, I ran it as root, though I suppose I should change that now), and I have noticed the issue still applies even to other non distributed- computing cpu loads:
"I tried to reproduce this using a simple busy loop in bash, and with 'yes', and by using cat /dev/zero or cat /dev/urandom > /dev/null, each niced to +19 and SCHED_IDLEPRIO, but for some reason, these did not create the same sluggishness that folding@home creates. In addition, these loads did not show up as 'nice' in my Gnome system monitor panel applet; Instead, these processes showed up as 'system' load, and they also sped up my CPU despite cpufreq being set to ignore 'nice' loads."
Therefore, this is not just a boinc issue.