Post a screen shot of Pad assignments.
What are these padstacks, a non-plated through hole! Do you have any land around the drill hole? If just a drill hole, is the drill hole colour set the same as your background colour?
An example of the above is shown below:
Hole1, drill hole colour same as backgorund.
Hole2, drill hole a different colour to background.
Blue ring is to show where hole is for this illustration, as can be seen a hole with no pad can be made to look invisible if its colour matches the background colour.