Ah if you are using advmame, then the syncs are less likely to be the problem - as I think advmame has total hardware control of the output signal being generated....
If the vhold is more sensitive, then either the jpac is buffering the output vga signal to stick to a certain vertical sync over a range of vertical syncs from the card, or as you mention it could be down to voltage differences.
My understanding of how the jpac works suggests to me that its not changing the voltage levels much, but I could be wrong.
I suggest emailing Andy Warne (Ultimarc) for advice, he would be more knowlegable...