I get that the bottom PCB is ground, but without the vias the top doesn't get to the ground. It is hard to see from the pictures on UG-095, but I believe there are vias under the package and closer to the device as well. For those frequencies I would expect to have some good vias so the grounds at the device are truly grounds. You can take a look at the gerbers provided here (http://ez.analog.com/message/68181#68181) and see how close your layout matches theirs. Also, have you checked the state of the lock detect? It should be showing an unlock state. How about the SimPLL results, do they show good phase margin for low and high frequencies for your design?
EDIT:
BTW, what are you tying to achieve (what are the parameters you're trying to hit)?