It could be a relatively rare bug used in the libraries for writing to the SMC, perhaps, since its happened to me on several occasions, but not yet on Castaway - sorta. Snes9x shoves up a load of errors if you turn off during a write that stop it being recognised, but that's predictable. On the other hand, I was playing SMS32 of all things (Phantasy Star Gaiden, I think) when mine was unformatted.
I have had one error from Castaway where the GP32 wouldn't recognise the card (this is back with release 3, and on a disk that image that works fine now - but can't remember which one; probably a Pompey Pirates early number), but thankfully I've got an SMC reader which did - interestingly there was a directory in the root called ".trash" - which given the 8.3 format limitations could have had something to do with it. I didn't try; no saves, so I just re-formatted, but it could be something to do with that. I think there was some other thing too, but can't remember what.