Your DB us corrupt. Delete it an it will automatically get recreated. Eventually
Tried this already, everytime I completely wipe PS3MS off of my hard drive and resintall.
I just unchecked the Enable the Media Library / cache and now everything seems to be working as it was before. I just read the documentation and it seems that with this checked it updates the PS3 data in real time, so with this unchecked will I have to add everything manually and reset the media database in order for new files to appear?