I had that problem for some time (up to about 6 weeks ago), but it's okay now. I usually just wait for a minute or two, then unmount the volume either by right-clicking the icon or with a truecrypt -d. If I try to unmount immediately after closing the affected application, I get the same error message ("Device or resource busy").
When I had the problems I used a script that contains this:
su -c 'umount /media/truecrypt9 && truecrypt -d && rm -rf /tmp/.truecrypt_aux_mnt1/'
Entered my root password and all was well. But, as I said, that's no longer necessary.
Hopefully simply waiting for a minute and then unmounting will solve your problem.