You can force the file system to unmount before plugging in the USB, that will make sure it's free for the remounter. To do that, in an xterm on the device, type:
If unmount complains, then the lsof command XiliX posted above will show you what's using it. If not, you can then plug in the USB and it will connect to the host computer. You may want to do a disk check once you mount it on the computer, since file system corruption can cause this odd behavior sometimes.