Well in case it can help someone else out, I got it to work by exporting to a preferences.dat file then importing that file. Somehow that made it work so go figure...it's just nice to have my shortcuts back.

Thanks for the comments guys! Anssi - I actually didn't have too much say in the design on this one, just did the model and some presentation work for it. I'm not sure I fully understand what you mean by the addition introducing it's own symmetry but I can sort of see what you're talking about. The original idea was to tear down the existing house which is really in poor shape. Due to the requirement of keeping it, there were a lot of additional factors that had to be taken into account.