As a side note I also have no playlists now on the player after it boots (they used to be there).

Right, after you delete the playlists, you must perform a synch with Emplode to get it to rebuild all that stuff. I believe that's in the instructions.

Note: If you have any third party programs, like tetris or pac-man, running from drive0 in AC mode, you will not be able to synch because it can't mount/unmount the drives. Although your serial log doesn't seem to indicate that's the case.

I noticed it said this:

EXT2-fs warning: checktime reached, running e2fsck is recommended

So just for the heck of it, do the manual FSCK and then synch once with Emplode. See if that fixes it.