I ran a chkdsk and it stated it was correcting the upercase file. Out of complete curiosity I Googled it but couldn't find any info. Anyone know what this file is?
It stores a mapping between lower-case letters and upper-case letters (so as to provide case-insensitivity). Details here: http://blogs.msdn.com/b/michkap/archive/2005/01/16/353873.aspx
And this one may apply more specifically to you: http://blogs.msdn.com/b/michkap/archive/2007/12/27/6875879.aspx, and links to this MSKB article: Error message when you run Chkdsk.exe on a Windows XP-based or on a Windows Server 2003-based computer: “Correcting errors in the uppercase file”