|"Only settings in the BIOS that were changed was the boot order (HDD0 instead of HDD1 which didn't work anyway)"|
That's odd, in the other thread you claimed it worked?
"CPU isn't throttling"
OK, have to take your word for it. I assume the idle temp is below 40C?
"Let's not forget the initial point of this thread, which was whether repair installations make Windows slower"
I believe that was already answered. No, a repair install will NOT make Windows slower, but it does "reset the clock" so to speak. Any Windows updates that were installed prior to the repair are replaced with whatever versions are on the disc, so there may be "slowness" in the beginning as the auto-updater plays catch-up (assuming you have it enabled). And as stated by wanderer, the repair is for the OS, it will not fix problems unrelated to Windows.
Did you tweak XP for best performance? Things such as disabling indexing, disabling the majority of the visual effects, disabling System Restore, etc? Have you ruled out a hardware problem? Did you disconnect the HDD with Linux on it? I think they are IDE drives, right? How are they connected? Generally, HDDs should not be connected to the same IDE cable/channel. The XP HDD should be the primary master, the Linux HDD should be on the 2ndary channel.