A few times now I tried reinstalling Windows 98SE but every time the installation goes fine, boots fine but it seems every time I put some files on the machine it will get stuck on boot after the Window 98 splash screen with a blinking cursor in the top left and the whatever was on the screen before the splash screen.

Files are mostly things like drivers, benchmarking programs and a few games. This sometimes happens when nothing is installed, but sometimes rebooting for installations works fine only for it to get stuck again after a hard power down. And at least once Windows booted fine but got stuck when trying to open the C drive. Deleting the files also doesn't work and the files came from my previous install.

Safe mode works fine.

What's the best way of finding whats going wrong.

Specs (not currently near computer so going from memory):
K6-III 450 CPU
Voodoo III PCI
Aureal Vortex 2
Awe 32
ESS audio drive card
200GB harddrive