card problems with synths in subfolders?

Since I started arranging my synths into subfolders, there seem to be some issues. At first it was working as normal, then I noticed it (quickly) said something about a file being corrupt on startup, and an XML file named __STARTUP_OFF_CHECK_SONGS appeared in the SONGS folder. Soon after that, one startup it said the card was corrupted, and I lost everything after the previous backup.

This was the card that came with the Deluge. I bought a new SanDisk Extreme Pro 32GB card, and I've got it loaded up with all my backed up data, with synth presets organised again into subfolders. Booted OK, I created a song, then backed this up. When I put the card back into the Deluge I saw the quick 'file corrupted' error again, and now it seems the __STARTUP_OFF_CHECK_SONGS.XML file is back (it seems to be zero bytes). I'm backing up often but I'm very wary of the card being lost again.

I'm not sure if this is an issue with the synths in subfolders, but I never really had any problems before. Having synths in subfolders (e.g. Pads, Leads, Bass, etc.) now seems essential, it was very tedious to scroll through synths alphabetically looking for something suitable. So just going back to the default all-dumped-in-one-folder arrangement doesn't seem like an option. But this feels highly unstable.