Do you have a SECOND holding tank, or do you mean the holding tank that is part of the porta-potty? Although I'm not familiar with your setup, typically a porta-potty uses it's own holding tank, while a "flushing" potty will have a separate holding tank. Can you verify this?
Aside from the accurate comments of clogs in one of the lines/vent, there may be a Y-valve to divert the effluent between the pump-out fitting and the macerator. If it's in the macerator postion, pump-out won't work. If this is the case, and there is not a second holding tank, the reason the potty won't drain is because it's full and backed up... from the potty all the way to the seacock. This means you will need to pull the boat, put a bucket under the seacock and then open the seacock to drain the system.
In any case, a macerator (whether it's good/bad/clogged) shouldn't affect pumping out since it's effectively on a different "circuit" than the pump out circuit.
EDIT: Forgot to mention... check your manual - there's likely info in there about doing pump-outs vs overboard discharge, along with the various types of systems that were an option on your boat (for whatever model year you have).