Get a cheap Neo Geo 1 slot board to test, doesn't even need a game.
No VGA video connection on Neo Geo boards. Hence the suggestion for a board like Tekken that has 15khz output on a VGA connector that can hook up directly to his NNC.
That said, haven't had any issues here with direct VGA via CRTEmudriver to my NNC (PFX) so far.
Out of curiosity, did you enable composite sync in Atom-15 or VMMaker? I can't get it to work at 15khz RGBHV (default) or after I enable composite sync and rerun all the modes. I suspect, I have to pull pin 14 on the VGA cable once composite sync is enabled.
Seems to be subtle variations on this chassis. Like mine can't sync properly to a Taito F3 board on the high impedance connector. While I've seen it work perfectly fine on 300wins' Sanwa PFX.