@voljega
it just occurred to me that I may have to edit the cmdline.txt as per my previous post a while back:
https://forum.recalbox.com/topic/4630/mapped-2p-buttons-don-t-behave-correctly/15

apparently, the cmdline.txt got replaced during the upgrade that had my manual settings in it. Going to back and update it again and see if that fixes the problem again.

as per the link.. the fix is in 4.1 (and not 4.0 Final)...

will keep you posted on my journey on this topic.