Large project? I mean at least 50 tracks and lots of FX...
All sorts of weird stuff starts happening when my projects get large. There's a bug with the metronome not sounding - you have to disable FX then re-enable.
Doesn't sound like your issue though.
I've had erroneous track behavior on the very first track in a project where it stays hidden even though track manager says its displayed. The track was visible however in console view so I dragged it away from position 1 and then copied everything to a brand new track. That seemed to fix it.
Mike.