At first, I figured this was due to the Dingux Fat32 write corruption bug. But now I realize that this pertains to both internal and external storage, and even occurs when I'm not running Dingux.
So, I did a chkdsk on both the storage volumes, and found that the savegames made by the internal emulators were the cause of the problem, as they had invalid time stamps.
Now, I wonder whether the absence of a clock in the Dingoo might be the cause of this 'dirty' situation? It's annoying, seeing I haven't been able to get rid of those pop-ups every time I saved a game state & connected the Dingoo again.

(Then again, I'm not completely sure it's completely absent, as I can't really make out this information.)