I have run into a problem dividing rooms that are on levels with only 3' of elevation difference. The dividing line wants to draw on level 1 instead of level 2 which is +3'. I have set the working plane to level 2 in all views and the line will still appear on level.
I have run into this before (I think). I ended up going to the plan view of the level that the room line should really be in and create the room from that plan. Perhaps that will help you?
I created a new view with very restricted view range and then copy and pasted a previous room dividing line in.
What is most frustrating is even though I have selected the correct reference plane in all ways and views I can find Revit insists on drawing the room dividing line on the wrong plane.