Start the game you want to play, then...
Go to options - configure graphics plugin - rom settings
Type 450 in for width and 240 in for heigth.
This makes the game playable, but it is not really a solution since you have to do it for every damn game.
If anyone out there knows how to FIX this problem without having to change all games settings, an answer would be greatly appreciated,
BTW - The steps are for Jabo's Direct3D6 1.5.1