@vic-viper-001 Well, now I feel like a complete moron. All I needed to do was re-install LzDoom, and overwrite the new lzdoom.ini with my old one.
Everything works again like it's supposed to.
@mitu
After some time thinking about it, I did choose my words poorly.
Instead of choosing one by one, you would gain time choosing to start and going out to grab something to eat or go to a movie or wherever, you get it.
But I understand you, and messing around on this files maybe would create some bugs...
Since the native menu system is based on a menu rendering library not available in Retroarch (libpicofe), the solution is to map all the missing options into the Retroarch Quickmenu. Currently, only some of the options are mapped to the Quickmenu.