Personally I think it is Rockbox, specifically recent builds. I installed Rockbox when I first got my iPod 5g, and until two days ago I was running an old unsupported build (senab's, fromm August). I just learned how to build it myself, and loaded on a much more recent daily build. As soon as I did that, it started having the problem described here about every 2 to 3 times it was powered off then on.
I suspect it has something to do with the state Rockbox leaves the iPod in when you hold Pause to power it off, since that's the only thing I can think of that would do this with what I have and have not changed (I didn't re-flash my iPod when I updated the build, I just made a new .rockbox folder).