Re: Is there a way to have a pad create to a plane on one layer and not another?

First, are your plane layers defined as split/mixed planes?  If you want both agnd and gnd nets on the plane it needs to be defined as a mixed plane.

"My goal is to have layer 2 be a plane with agnd and gnd and only connect to agnd at those 2 points." - It sounds like layer 2 has a different net defined on it then agnd where the connections are not being made.