In BS.Player's "
Options > Preferences > Key definitions & WinLIRC",
shortcut keys can be (re)defined
separately for [Windowed mode]
and for [Full screen mode].
Maybe they're not the same in your setup, so that's perhaps causing your problem in full screen mode?
(I suppose you already found the info inside the folder "sdk" (and its subfolders), which can be found in BS.Player's installation folder?)