Hmmm.
Just found this:
There is an issue with saving custom keyboard binds on localized Windows version (or on localized keyboard layouts). Manual keys mapping is required.Mouse buttons and scrolling wheel is not assigned to any action.
https://www.pcgamingwiki.com/wiki/The_Operative:_No_One_Lives_Forever#Remapping
So I guess this always was an issue on newer Win versions, I just forgot about it, because I haven't touched key configuration for years.
(So I guess you won't be looking into this nolf bug, seeing as you moved over to nolf2 modernization?)
PS:
I tried the "+windowed 1
" command line parameter from the linked page for the issue I mentioned in the other comment. But apparently modernized is incompatible with it because I got an MFC client error and failure to start the game.