Make sure the Hole To DRC's are enabled (they are not by default because the pad would normally take precedence). Go to Setup - Constraints - Modes - Spacing. You will see that some have ticks and some have grey boxes (not all checked). Now put a tick in the Spacing DRC Modes twice, once to turn them all off and agian to turn ALL on.
You are normally warned to turn these on when you enable the unused pad suppression.