Best fix for any Windows issue is one of the following:
http://www.getfedora.comhttp://www.ubuntu.comIf you really really must run windows (can't think of any reason why you would... I run everything on my Fedora 12 installation with no issues) then I would grab a linux boot CD, such as QParted or similar and boot from that (even a Ubuntu live CD would work) then run fsck from command line against both your USB drive and your Windows partitions... Then when back in your inefficient NTFS Windows partition run Defrag
Of course you could go ultra geeky and install a BSD Flavour!
**Edit** The post is kind of tongue in cheek, I know most people prefer to pay the extortionate Windows licensing costs and prefer the bulky and slow interface to windows, therefore if you need any windows based help I do know quite a bit about it (Run a number of windows web servers... they are customer servers and they program in .net *shudder*) and can offer some help based solely on windows