Although the image looked fine on the LCD, it had a "signal error" and it displayed fH: 29.0kHz fV: 41.0Hz, but again,
Yes, this game is supposed to run at 41 Hz. GM is outputting the right refresh but obviously your monitor can't handle it, although its specs mention 40-80 Hz, or maybe an extreme adjustment is required which would leave the other frequencies out of sync. In the best case 41 Hz will show a horrible flicker. So it is best to just limit the lower frequencies to a more reasonable value, like 50 Hz. In order to do that, create a custom set of ranges, based on the current ones your using, like this:
monitor custom
crt_range0 15250.00-18000.00,
50.00-80.00,2.187,4.688,6.719,0.190,0.191,1.018,0,0,224,288,448,576
crt_range1 18001.00-19000.00,
50.00-80.00,2.187,4.688,6.719,0.140,0.191,0.950,0,0,288,320,0,0
crt_range2 20501.00-29000.00,
50.00-80.00,2.910,3.000,4.440,0.451,0.164,1.048,0,0,320,384,0,0
crt_range3 29001.00-32000.00,
50.00-80.00,0.636,3.813,1.906,0.318,0.064,1.048,0,0,384,480,0,0
crt_range4 32001.00-34000.00,
50.00-80.00,0.636,3.813,1.906,0.020,0.106,0.607,0,0,480,576,0,0
crt_range5 34001.00-38000.00,
50.00-80.00,1.000,3.200,2.200,0.020,0.106,0.607,0,0,576,600,0,0
If 50 Hz is still out of sync, try increasing it until it works.