My beloved HOTAS broke down ages ago [before i even bought Elite], so i am on a DS4..
However, i experience some troubles with modifiers as well... and also found a temporary solution to this..
I have set "O + digipad up" as "enable FSD" - but sometimes when first leaving a station upon entering the game, the "O + up" combo enables 'headlights' - which isn't even set on my pad anymore but just the "H" key on my keybord..
However, i remember an older, less fine tuned ds4 config i was rocking in which "O+up" actually represented the headlight function..
Solution for me:
Go to settings, check if everything is set in there as you want it to be [as for me, it shows "h" = headlights / O+up = FSD] - it probably will be set to your likings allready, just not working the way it's displayed under 'controls'.
Click apply [even though you changed nothing] - should be fine and working now.
Works out for me every time this happens..
Also, when you experience this, does "module priority" gets reset/bugged for you as well?
Happens to me, too, and i feel the 2 problems are somehow related to each other...