With a fresh Windows install, if there is something odd going on, it's usually faster just to start over than to spend a week debugging an issue that could very well lead you to do the reinstall anyway.
If you choose that, before you do the windows install, boot with a dos floppy and delete all partitions. Recreate primary, hard format it, then do a fresh windows install from there. Let it run for a day and see if the issue is there again. If not, install your apps one at a time, letting it run at least a few hours between, and check for that issue each time. Eventually, if the issue comes back, you'll have few enough variables that you'll know what caused it.