OK, this is a disaster. I have the same "every board twice in Board menu" problem as mem; I have inexplicable and inconsistent compile errors such as symbols multiply defined or undefined; I have null pointer crashes; I have empty sketches that keep reappearing... I'm going straight back to 0016.
My guess is that this is something to do with using the same library on two different boards, and it's caching things wrong, because a lot of the errors refer to files in tmp directories. I've tried deleting these, but the errors soon recur.
Please fix! Multiple windows would be nice, if it worked.
Barney.