There are a few threads with people saying they restored their e-mails and the program gave a "restore complete" message, but no e-mails showed up in the inbox. I had this problem and seem to have solved it.

The solution is very simple: use the Windows version! I was using the Python version on a Mac (unsupported), and it wouldn't restore either through command line or GUI. The Windows GUI works just fine, however. It's possible that running the Python version on a non-Mac box would work, too, but I think it's probably just a bug in the Python version in general.