Just thought I'd post my experience with two hosts running Ubuntu 64 and identical GTX 280 boards:

1st box, kernel 2.6.24: 25.403 ms/step, 21592.498 s, CPU time 2645.98
2nd box, kernel 2.6.22: 34.903 ms/step, 29667.695 s, CPU time 9.29

The second box was showing sub-par performance and extremely low CPU usage, even with no other tasks. After fiddling around a bit, I tried upgrading to Ubuntu intrepid:

2nd box, kernel 2.6.27: 25.390 ms/step, 21581.760 s, CPU time 2295.54

Performance and CPU usage is now on par with the first box. I may be jumping to conclusions here, but could this be caused by the introduction of CFS (Completely Fair Scheduler) in 2.6.23?

Anybody else seen issues like this?