Run a CHKDSK command (Check disk) from a Admin level DOS prompt, or from the Disk properties (Right click drive in my computer : Properties : Tools tab : "Check now" button in windows 7). This will check the directory structure, which sounds like the problem here. I am old school so I usually type this into a command prompt and if the drive was F: then it would be --
CHKDSK F: /F
I like to do this without the /F flag to start with, so that it is "read only" and you can see what issues are likely to be fixed if you run it in fix mode. What you are hoping for, most of the time, is "No problems found". For a USB this should run at any time assuming files are not already open, on the C drive you have to schedule it for a reboot.
Sometimes a drive will not appear at all because the drive letter it is assigned is in conflict. That doesn't sound like the problem here, but a look into
DISKMGMT.MSC might be a good thing too (type this into Start : Run). This will tell you how the drive if formatted and the partitions, and its "Status" (Healthy?).
Your USB might have gotten into this state by being pulled out at just the wrong time, and not dismounted gracefully.