I'm having this same issue. When putting the songs onto the board with the pc software, I renamed the track there first and then transferred, which helped with the name reverting back to track 1 problem. The problem is when I turn it off and the next time I turn it on, the audio from the songs won't play or show up as present on the headphone out mixing screen, but the audio is still stored on the board, because the audio still shows up on the screen, but doesn't play the audio at all. I wasn't sure if the flags disappearing was from my error in not saving it properly before closing down, but seeing that this is a serious issue, I'm not so sure its me that's the problem. It worked fine until I turn it off and the audio and flags are just gone afterwards, with the flags completely absent from the monitor screen and the audio visible, but not playing.
Also, I don't think the snapshots are saving individual set parameters from the pedal settings, just the on/off states for each effect pedal slot. For example, if I set one snapshot to have 70's chorus with a heavy effect and another snapshot with that same 70s chorus with a lighter effect, it doesn't save that change, it just leaves the setting on wherever I left it last for both snapshots. I can't imagine this is by design, as my much less expensive Headrush Flex Prime pedal can easily do this.
Otherwise, the Showcase feature is truly amazing. The first time I ran through a song, my muscle memory was so hard wired it felt wrong and strange to not hit a pedal to change my sound. To trust the machine seemed a bizarre leap of faith, but by the end of the song I realized how much easier it is to play and not have to focus on my foot too. Adjusting in/out levels on the fly is a breeze too. I know they released this feature early, so I'm glad to finally see it, but I probably won't mess with it again until this is patched up.