If they pulled OK before you upgraded pyTivo, and not now, then I assume that pyTivo is now passing them through as OK, but the TiVo is choking on them. Try marking the container as bad in the metadata, so that pyTivo will remux them -- add a line like "Override_container: foo". The push issue just sounds like the typical flakiness from the mind server, unrelated to the pull issue, and not actually dependent on the file type. And this is new behavior? If so, maybe try rebooting your router, then the TiVo if that doesn't fix it.