Actually, yes. I used to be an Apple Genius and whenever we dealt with two machines on separate LANs, that required NAT, there were so many problems with traversing the routers. We had to do manual setups with port forwarding or DMZ. Facetime seems have significantly improved with this (but was awful when it was iChat w/ Group Video chats), but Back to My Mac is still very problematic-- you can see this issue also by trying to Screen Share over iMessage to other people. In my experience it only has about a 50% success rate.

My home setup still doesn't work with Back to My Mac (and hasn't for years).