Non-hidden directory doesn't show in Explorer, but exists...in some sense(?)

I'm using IMAPSize to backup my mailboxes. The process just dumps the contents of your mailbox into .eml files on your disk. Anyway, the first mailbox I backed up shows up as I expect. However, the next one doesn't show in Explorer and, if I enter it in the path, it tells me that it doesn't exist.

However, IMAPSize is insisting that the files are there. (A lot of disk writing was being performed during the operation.) Moreover, the directory does appear in the Windows directory dialog and -- as I have GNU tools installed -- it shows in ls (but not in native dir). I can't cd into the directory, but ls does seem to be able to access it (and, indeed, the directories and files I expect appear to be there).

Also note that the timestamp and filesize of backup.db are different in the dir and ls -l output.

In short: What the hell is going on here and how do I fix it!?