Justin, I had a wierd one the other night that may be related to your post.
I have 3 tuners and often have all three recording happily away no problems. The other night I had one scheduled recording happening and SWMBO was watching a bit of live TV when she decided she wanted to record it to watch later. I hit record and got an error message saying I could only record one channel at a time.
I then set up a manual record to start in one minute and behold it recorded.
Would this be related to this watch / preferred thing of which you speak?
(Although i must confess I'll need to read you post through again a bit slower to get my head around it.)