Okay, so the issue then is that I cannot appoint myself Margrave of BR, because I cannot take an estate in the region (when transferred over it joined the other duchy and so I can't be lower than the other Duke) and so I can't make myself the Duke.
Other than resigning from being ruler, is there a way to get around this? Seems kind of severe to me...then again, this game has gone to great and extreme lengths to do severe things to me 
Multiple threads have been written on this. It's extremely inconveniant and requires massive acrobatics to successfully become duke after becoming ruler. For example, if you get elected to the position, the game only gives you 2 hours before the allegiance "fix" code kicks you out. Splendid, isn't it?
There's no good solution. All means to achieve this are extremely gamey. You can either step down, let someone else become ruler and get him to make you duke, and then seek to become ruler again. Or, you can promote someone else to become duke, and ask him to step down to make yourself duke. Both of these "solutions" are borderline placeholder situations, which is against policy.
But until the devs decide that it's be better for the allegiance auto-"fix" code to create a new duchy for the ruler instead of kicking him out of his lands, it's pretty much the only solutions available.
