Probably that particular screen res is used only for Neo Geo and not (most of) the other ROMs you have.
Are you using a multisync PC monitor? You probably want to adjust that rather than anything else.
On my Sony monitor I was able to centre and size every screen res individually, so boot up a Neo Geo game, adjust the centering and size, and hey presto all neo-geo games would be fine. (and the same for verticals, vectors, old low-res ones, etc.) The cool thing is doing that did not screw up any settings previously made for other screen resolutions.