Thanks again, man. It seems I've been editing a core-specific cfg file which overrided the "all" retroarch.cfg file but I couldn't edit it from retropie, had to edit it by SSL. Now all my binds are as I want 'em.
Is it only certain games every time or is it random when it works or doesnt? If it's the same games every time I'd say that it could be possible those games have a non lr- Mame emulator associated with them which could mean the bindings are loaded from a separate cfg whereas all of the lr- emulators use the global retroarch cfg. You should be able to spot check a couple in the runcommand splash screen menu if it's enabled.