Doc, it hurts when I do this...

"Don't do that."

One thing I know is that checking the media (fsck) takes up a good deal of memory, in fact the player app turns swap on before it does the fsck to avoid such a crash.

I have no idea why it would cause a crash. I also don't really want to test it out because I value my music partition and crashes while fsck is running are bad for your music's health.

So, like, quit out of Emptriv (and all other user apps, I would recommend) before you sync.