Unfortunatly this is not an uncommon dilema. Quark 4 does indeed work fine for many in the industry but it was never intended to be a proper venue for PDFs.
Just cause someone wrote an extension to add some for of functionality does not mean it is fully functional.
If your boss has deemed it appropriate to stick with a working system, you are kinda stuck with it too. You are not alone, though.
However, your boss is also straddling you with the limitations of that system and can't complain. Accepting PDF ads without the software to verify or fix/troubleshoot them is ill-advised.
Long live the Sofa!!!