I was just in the process of testing this again. In arcadeosd when both vsync and hsync are negative the modes won't display. As soon as I change them both to positive the mode displays. Still won't work in groovymame but they will test ok in arcadeosd. I've tried the old vmmaker but it still has issues. I'll keep going trying to figure out why.
So are you trying all this with new vmmaker?
If that's the case, enter the monitor presets settings, and edit your current crt_range with +hsync and +vsync. Then generate and install the modes again.
monitor "ms929", "Nanao MS9-29", "4:3"
crt_range0 15450-16050, 50-65, 3.910, 4.700, 6.850, 0.190, 0.191, 1.018,
1, 1, 192, 288, 448, 576
crt_range1 23900-24900, 50-65, 2.910, 3.000, 4.440, 0.451, 0.164, 1.048,
1, 1, 320, 384, 0, 0