I don't quite understand this. The '09/'10 bikes have about an inch less suspension travel and around a half inch less ground clearance but they have a slightly higher seat height than the '06/'07 bikes?

Did the frame get taller or something?

 

Different wishbones and spacers in the fork cartridges make for shorter travel but same seat height. You can remove the spacers but it is a hassle. You can change the wishbone as well. I am pretty sure that this is the case.