From what I've seen on this thread, I haven't run across a solution to this issue:

Before R:TW was updated via the MAS in May, EB was working perfectly fine for me -- however, after the update, the game will not launch EB at all.

I've looked through the files and everything is still in the right place. Even with "-mod:EB" entered into the Advanced tab, it still launches straight to vanilla R:TW. Barbarian Invasion will not even launch when selected.

I've toyed around with it a bit but I'm hoping there may be some other solution out there before I have to wipe everything and reinstall it. Any ideas?