Well, I'm not sure. I tried the same SETI WU on Linux and on Windows. It was going to take about 30 minutes longer in Linux than in Win98 at the same point, though I never checked the completed times. 'Course there were several differences:
Linux: Win32 partition
Win98: ramdisk
Linux: V2.4
Win98: V2.0
Linux: priority 19 (lowest)
Win98: priority 8 (normal)
So anybody know what, if anything, went wrong?