I know this is a bit of an old thread, but I have the same issue. LB controller automation works, but not in BB. I am using an xbox360 controller and in MAME I can't exit a game using the "select/start" combo that I use in LB with no trouble.
In MAME itself, I am unable to configure an "exit" key combo either using the controller. There as well, I have to use a keyboard key "escape" to get out.
I've thought about using xpadder, but it seems very finicky to setup and I don't believe will let you use a 2-key combo to trigger the "escape" key.
Any ideas?