Your disk is corrupt. Make a backup first then command-r boot to recovery and from there start Disk Utility and do a repair disk and see if that fixes the disk errors.
After that restart and use the computer a while then start Disk Utility and to a verify disk again and see if more errors are popping up.
These disk errors may account for the odd and constantly changing space used readings you were getting. It could be a failing disk.
I didn't think to post on a help forum but ended up just getting TheMiniDrive and putting all my photos and music on it. They have a microSD adapter version but I got an integrated card that came with 128GB on it already