The folding rig I leave at work is Linux. What a pain in the ass. The two 5670s in my sig rig are now in this folding rig (need to update that, yeah). I bought a 6870 and it's dramatically faster, but everyone knows that.
Collatz takes significantly longer. I believe this is at least partially due to unoptimized drivers, but don't have much basis for that. I say partially because at home I have an i7 950 and here I have an oldschool AMD X2 3800. The processor difference must make some difference.
Rawish data:
Each 5670 on Win7 Pro on an i7-950 stock would finish the long collatz in about 1:40.
Each 5670 on Ubuntu on an AMD X2 3800+ finishes the long collatz in about 2:20.
I think some of that is processor, some of that is drivers. Probably most of that is drivers, but I can't prove that. It'd be a pain to dual boot Ubuntu on my home computer and swap cards back to get exact numbers of drivers-only difference. I know you can change the interval that the collatz optimized program polls the processor, and you can force it to load multiple work units into the GPU simultaneously if you think that it's under-utilizing the GPU. By my heat output, I think it's still maxing them and the drivers are just crap.
I've also had other problems with:
Wed 06 Apr 2011 02:09:30 PM PDTCollatz ConjectureTask collatz_2368949436103904700776_824633720832_1: no shared memory segment
Wed 06 Apr 2011 02:09:30 PM PDTCollatz ConjectureTask collatz_2368949436103904700776_824633720832_1 exited with zero status but no 'finished' file
So take a look and make sure you're not getting stalls due to these sorts of errors. I have to pause GPU while I'm on the computer or I get these. It takes a minute to restart after the last checkpoint for each of these, which will add to your completion time.
Finally, I'm still mostly a Linux noob so take this with a grain of salt. Any advice for me is appreciated too. Goodluck!