I don't know if there is any way to fix it in AC11 (not to say there isn't I just haven't needed to). This probably happened because some of your elevations had their marker type set to "Section" in AC10. If you change this in the AC10 file and reopen it in 11 that should fix it for you.
I too question the sense of this new tool. It makes things slightly easier by letting us have default markers set for each, but I have always considered elevations to be sections that don't happen to cut through the building (or sections as elevations that do). Besides, many sections also include partial elevations (particularly in "U", "H" or "O" shaped buildings).