I vaguely remember a couple people running into empty dungeons, but I don't think it was related to installing a patch.
It is possible for the third dungeon level to be empty, since quest items and monsters are randomly placed.
Quests auto-completing is a new one, AFAIR (there are a couple quest objects that will trigger the quest log update icon when they are moved, but that is just cosmetic).
The BF quests (and dungeons) are optional, so there is no timeline on when they should be done (though if you wait too long you might stop getting experience for weaker monsters), so that would not be the cause of your problem.
I would recommend you re-install the patch when you get to the end of act 1. Entering act 2 with the patch installed should give you a fresh start, and hopefully avoid whatever glitch caused the problem the first time.
Before installing the patch, try deleting the files within the dynamic folders (not the folders themselves, though);
'
..\Beyond Divinity\Acts\Act1\Dynamic', '
..\Beyond Divinity\Acts\Act2\Dynamic', etc.
These folders are used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied to those folders when you save a game. The files will be re-created as required the next time you start Beyond Divinity. If there was a corrupt file in those folders, deleting the files should fix the problem.
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