Well, if you are using XP (not Windows 2000), you can try the fix from Microsoft. Look in my signature for a link that says How to Delete Your Upper and Lower Filters. Click on that and it will take you to an article from MS, where you should click on the Fix It button to start the process. May not help, but won't hurt to try.
A fresh install will probably help if this is a software problem. If the drive itself has physical problems, then no, it won't help.