I'm fairly confident the issue is that you are mounting stuff in /media and /media2. This is not recommended, not supported, and can create unexpected results. I had to have someone stop doing just that last week so that we could delete almost 5GB of temp files that were hiding there.
You should unmount those locations. You'll probably find hidden files in /media and /media2 that weren't there before. Delete or move them and your space will be fixed.
Then don't go mounting stuff on the FreeNAS again. ;)