Okay, I guess it's most on my end then but could someone try the following (getting complicated lol):

1)Start BSPlayer
2)Start a movie (no matter what format)
3)Bring up the "preference window" (Ctrl+P)
4)Go into full screen by "double clicking" your mouse
5)"click" ones to show the "control window"
6)Now exit full screen by again, "double clicking" the mouse (not Esc)

To me the "preference window" is now hidden behind the video window no matter what I do, if the "control window" is hidden however (automatically or manually by clicking) there's no problem.