Boot Loop after BIOS reset

Some kids at the school I am stated at put passwords on the BIOS, so we used the pins next to the BIOS chip to reset the BIOS.
This has worked to clear the BIOS passwords, but it has had the unfortunate side-effect of putting any computer we do this to into an endless boot loop.
The computer gets as far as a screen where an option to "start windows normally" (among others) appears. Sometimes the windows xp logo can feintly and briefly be seen before the computer restarts its self.
I have re-created the issue with computers that didn't have passwords on the BIOS by resetting it anyway and the symptom persists.
What am I missing? I've tried using the BIOS options to optimize the setting and I've also take a compter that does boot (same make / model) and mantually copied over the settings in the BIOS.
Still can't get it to boot.
I can flat load linux to it, but windows won't take, either via a PXE boot or disk. The install seems to go so far as to unpacking the files, but isn't able to boot into windows sufficiently to do the rest of the install.
:s
Any help would be greatly appreceated as we now have 11 out of 24 computers doing this.

I would like to add, whilst I was using the pin clips on the pins near the bios chip, I let the system run until it would beep. During this time, the CPU fan ran really really hard. Have I damaged the CPU somehow?

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