Very odd. Looking at the code, that shouldn't be possible.
Were you able to rest in the bed? Did the game give any kind of indication that some part of the base quest was complete?
Not that is needed I restarted the game and played it 3 new games last few days to play all 3 evil mode character for the 1st game I had that problem I still have that saved in slot 1 quest was not completed and all three chest was opened so couldn't open the chest again thus unable to complete the quest at all.