[Prof Yaffle]

I suppose it's possible that tvheadend has auto-detected the muxes but either got the config wrong or the config has changed since they were discovered. You can see the mux configuration in the web interface - you could delete teh mux and let it re-add. Or, if you're up to it, you could simply shut down tvh, edit the config files and restart. QAM64/T2 channels should play fine play on that tuner.

EDIT

They're not time-shared channels, are they? Broadcasting for only part of the day?