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?
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(I suppose you already found the info inside the folder "sdk" (and its subfolders), which can be found in BS.Player's installation folder?)