Registry errors

I just put my new computer together and it was working fine until yesterday. I loaded the drivers that came with a flash drive I bought, and after I restarted my computer, the following error message came up.
Windows has found an error in you registry and will attempt to repair it
It restarted, tried to fix it, and it froze towards the end of the program. I rebooted and it came up again went through the process, and supposedly worked this time. The problem is, every other time that I boot up, the registry error pops up when my main screen loads.
Would reloading Windows be my best bet here? or would one of the registry repair programs out there work?
Thanks

It depends on how much new data you have on it. I don't know much about registry repair programs, so my advice is that if you can back up or don't mind losing data, go ahead and reinstall windows. If you do that, make a backup of the registry before you install the flash drivers again. You can do that by

-Clicking the Start button
-Clicking Run
-Typing regedit
-Click ok
-go to File>Export
-type in a name, like backup
-make sure the All option is selected in the lower left, instead of Selected Branch
-Click Save