I concur; I thought it was going to be like that/didn't know it could be filed as a bug - before the patch, it wasn't the case at all, I look forward to see it fixed eventually. Alt-tabbing is fine but after some point and/or if you have 48597749 windows open, it gets a bit difficult.
Edit: And honestly, I don't know a lot about FLUF except that it helps editing a bit the game.