I have this problem too, but it seems that there’s a very simple workaround:
http://i.imgur.com/Rkd4QwJ.png
The only annoyance is that when you open up your level it won’t work right away. You have to play your level, and it will start working, then, when you go back to the editor it will work there as well from that point.
By the way, not only the ConsoleVariables.ini isn’t working anymore, but the Fixed Frame Rate seems to be broken as well.