Yes, I have seen this bug, too. It's happening with osso-media-server as backend if you pause a file for some time. After resuming MediaBox tries to seek to the position where it left, but somehow osso-media-server doesn't get it.
Could this be related to the trashed SD card? It sounds like MediaBox cannot find the files and thus doesn't list them. Reinstalling the package shouldn't have any effect on this. Removing the .mediabox directory is the best you can do to reset the index. If removing it didn't fix it, then the problem was not with the index. You mention that everything appears in the podcast directory. It would be interesting to see what the file manager says about this.
In January, I suppose.