It might be that you damaged the usb port. Some are quite flimsy. Three out of the 6 on mine are dead now.
It is also possible that the drivers got messed up with the new software being added. You could try and fix this by reinstalling the motherboard drivers, as these include the usb ports. You should have a disc with them on it that came with your pc. As a precaution, you might want to back up your files onto a cd first. I do this regularly just incase anything happens.
If none of the above work, and you are about to throw it out the window, never fear, you can always reformat the drive and have a clean slate, though this takes time and is annoying to have to do.
