My thoughts on that find ...
The difference on amount of RAM on graphics cards becomes fairly small if you use compressed textures, because then the AGP / PCI-E16 but have plenty of bandwidth for swapping textures between main RAM and Graphic card. And since the game isn't Graphics card centered game anyways, you end up with the CPU bottleneck once again.
Try and see if you have compressed textures on. If they are and you turn them OFF, you ought to see a bit more of a difference due to texture trashing. No idea how big the Textures really are though, SOE never mentioned that AFAIK.
Does your old CPU fit in the new mainboard ?
That would be an easy way to test the difference on CPU's.
Unless you can Underclock it ... that would be even easier.
You mention that you run the 6600GT on the faster CPU platform, that also has more DDR-RAM.
The difference in Main RAM on the two systems ought to make a difference too.
Might be part of what makes the machines so identical.