Hi DeathMonk,
It seems you sorted it out. Anyway, if you want to have a progressive 640x480 resolution, you can edit the mode definition in ReslList.txt before running VMMaker. By default, it's defined as interlaced (640x480@30) change @30 by @60. Then use a monitor preset that's capable of doing that resolution as progressive, like a tri-sync preset. Same for 800x600.
Alternatively you can use Winmodelines and add the new modelines that you want or edit the existing ones.