Don't know if this is the problem with your system, but when I installed my Adaptec 2940U2W with an Atlas 10k III, I had same kind of problems, low write performance. Naturally I tried enambling write cache for the drive -> No help. Then I noticed the write cache checkmark keeps popping of every time I reboot. Checked 2940U2W bios, Write cache was set on.
When I set write cache setting to default (NC or auto or something like that) and booted to windows, I could set the write cache on so that it sticks. And now my results are OK.
Are there some issues with Adaptec card forcing write cache on or is it just my setup?