One more idea I have how to fix this: Remove (once again) the ~/.config/gpodder/database.sqlite file. Move all _files_ (not folders or folder contents, just the top-level files) from /media/mmc2/gpodder/ to ~/.config/gpodder/. Make sure the download folders (with strange md5 filenames) are direct subdirectories of /media/mmc2/gpodder/. Start gPodder and chose to migrate the database. This should work.

If not, and if you don't mind me seeing what you are subscribed to and what you have downloaded, please tar up your /media/mmc2/gpodder/ folder (with the file names intact, but you can replace "big" mp3 files with zero-length files by doing something like echo -n "">file.mp3 - obviously BACKUP all your files first, because they will get truncated with this command!), make sure the index.xml files for each folder and the *.db files (from the old, file-based structure) and the channels.opml file are all included, and I will see if I can spot the problem locally here.