This is an older post, but it's still totally relevant to AdvanceMAME as of version .92. (and probably higher) Cheers to desmatic for posting the tip!
This problem manifested itself for me in a rather strange way. Because the SVGALINE driver didn't choose the wrong hclock every time, I was able to run almost any game without issue. Here's what I did notice while having the setting on "auto":
NeoGeo games (and every other game using the same resolution) had a slight hula effect. (hclock must have been slighly off)
Pacman wouldn't display in it's native resolution at all. (hclock must have been WAY off)
Once I made this change, suddenly all the games were rock solid stable on my WG 25k7191 with Trident Blade T64.
I wish I had seent his post before installing a new cap kit.
Oh well, probably needed it anyway.