Hmm, just guessing.

What about disk usage. And I do not mean free space but number of inodes! To be checked with
df -i

Mine does that too. But really rarely.
My disk usage is about 90% used (always get the warning). But inodes are not close to limit.

I have not really much music or pics on device. So possibly lots of small thumbnails?
But, again, just guessing...