I too use BD. I have a Studio with two ASD and a Dell 6K. Display position is never an issue - works 100% of the time. Occasionally (and for reasons I can't figure out) BD is unable to hold the size and position of my windows when I wake up the system. That will persist for a few days and then all of the sudden it's fixed again. I'm fairly certain if I wasn't running BD, the window size and position issue would happen all the time.In some aspects I've moved on from Mac. But the Mac I use at home I got rid of this problem by using an app called Better Display. Works perfectly and has options it Mac decides to reset the monitor settings.
For folks having these type of issues, I'd give BD a try.