USB 3.0 thumb drive causing system hang on shutdown

Hey guys, I just finished my build. Everything has been running super snappy and great until last night when I noticed that my system was hanging on the shutdown screen.

I used this thumb drive to install Windows 7 on this machine. I formatted the thumb drive to FAT32 and was going to apply the bootsect then copy the iso over when I realized that microsoft has a utility to do it all for you so I just used that tool. It gave me a bootsect error because I was making a 64 bit installer using my 32 bit machine. So, I downloaded a 64 bootsect and put it in my system 32 folder. Microsoft's boot disk creater tool worked flawlessly from then on. I installed windows, all my firmware updates, all my drivers etc. I've since erased the contents of the thumb drive (by opening it in computer and just deleting the contents) and used it to transfer a few files here and there. Sometimes when I try to open it immediately after plugging it in it gives me an error of something like "error you don't have permission to access this drive" (sorry I'm paraphrasing, I'm not home right now). Anyways, if I try to open it again a few seconds later it works okay. Soo, last night I was shutting down and I noticed it was hanging on the shutdown screen. It hung there for a few minutes then when I pulled out the USB stick it completed the shutdown immediately. All my drivers and firmware are up to date, and I install all the windows updates as they come.

So what do you guys think? Do I need to reformat the thumb drive? Is there some other issue that could perhaps be fixed with a hotfix or something? I don't mind to reformat the drive, I hadn't thought to do it until just now though (I'm at work so I can't until I get home).