Really puzzled by your monitor situation.
Much of the reason people use cabs is to get that "authentic flicker" of 15KHz CRTs. I would not be surprised to discover your old AGP video card was an ArcadeVGA from Ultimarc.
The question then becomes, why are you getting proper video output now? With your new system you are likely not using the AGP video card. And... you struggled at first.
Perhaps it's a tube and controller capable of 31Khz, which would be why VGA at 640x480 is working... but then... you will likely soon receive a call from your arcade owner saying that the sound is choppy in some games, and before it was smooth, or something. *puzzled*