Go to Tools. Options. Select the Split/Mixed Plane tab.
I f you have this box checked: Use Design Rules for Thermals and Antipads
Then PADS will go to the size spokes described in the Thermals tab and override the padstacks.
A co-worker of mine just ran into this. In Tools->Options under the Thermals Tab, there are a bunch of different thernals. Make sure to select the relevant thermal. I suspect for an internal layer you want Drilled thermals, Round to be selected then you just change the value in the dialog box.