So I just solved my issue.
Any changes that I make to mame.ini, be it using the UI or editing manually are being applied only the first time a game is run, when it creates the initial ini file for that game. Any changes I make after that are not being applied as it is drawing settings from the individual game ini files instead using the updated mame.ini settings.
I would have noticed this sooner but for some dumb reason, I was just using one game (final fight) in the rom folder to test the latest build. And whenever I tried a different build, the first thing i did was load the damn game before changing screen settings.
This explains the monitor not working, the preexisting ffight.ini was overriding my changes and loading the screen as 'auto'. As soon as I removed this, and manually edited it just to be sure, it all worked properly.
Is this intended behavior? I would have thought per game ini files wouldn't come into play until you manually went out of your way to change settings for a particular game. But I guess MAME design would prefer being fully configured before you start to run stuff.
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