Hi Rob,
I've noticed the flakiness too. I haven't had time to track it down, but it's quite possible that the new TiVo software has a bug making it miss the initial connect requests (and of course, it's quite possible it's our software too). I've been able to get around it by trying twice or so, and if that doesn't work, restarting the server.
Jim's talking about shutting down the TiVo server via "Services" hidden somewhere underneath the control panel. If you don't do it this way, it will reappear at inopportune moments.
The strange messages in Library Server actually are normal. If the TiVo can't connect to your machine on the TiVo Beacon port (2190), then (after many seconds) it will try to conect on port 80, the HTTP port. Since your library server is running on 80, it's getting the TiVo messages and saying "I don't know what to do with these"
j