two things come to mind...
1) see if your on-screen display tells you what your refresh is, i would be curious to say what it says...
2) i would try bumping up the pclock, see if it will show up correctly for you then...
Modeline "512x384" 19.72 512 544 616 648 384 391 396 404 -HSync +VSync
something you may want to try, if your NEC goes up to 50Khz, is to use doublescan. You double the pclock and use doublescan, you can test, and then drop the pclock and doublescan option when you go back to using the arcade monitor.
Modeline "512x384" 30.76 512 544 600 632 384 392 396 404 -HSync +VSync doublescan
my best guesses.