Drew - this is really simple. But you have to believe what you're being told. If the manifold is under vacuum (as at idle) it's SUCKING on the crankcase through the pcv valve. When it's sucking on the crankcase, one of two things can happen.
1) If the crankcase is completely sealed to outside air, then you'll pull a vacuum on your crankcase. The crank end seals and various gaskets (like Valve cover for instance) probably won't seal perfectly, so pull enough vacuum on the crankcase for long enough (long interstate cruise) and eventually you'll probably pull some air into the crankcase via one of these other paths.
2) If the crankcase isn't sealed (you have a breather or the stock hose to the throttle body) then you have a path for air to enter the crankcase to make up the air that's being pulled out of the crankcase through the pcv valve. The stock system is designed so that the make up air has already passed through the mass air meter for obvious reasons.
Put a breather on the stock system and you allow unmetered air to enter the intake whenever vacuum is present - i.e. - you create a vacuum leak. Some vacuum leaks are worse than others -- you can have minor vacuum leaks that don't impact idle or drivability that much.
If you want the stock pcv system to work correctly then put on a new hose/valve/screen/grommet -- buy the parts from the dealer as they fit better to eliminate leaks. Then reconnect the valve cover nipple to the throttle body and get rid of the breather.
Otherwise, cap the pcv port on the manifold, block off the pcv hole in the lower intake and put two breathers on. Be prepared for the oily mess the breathers will make as they dispense a mist of oil over the top of the engine. An alternative is to run hoses (at least 1/2" dia.) from each valve cover to a remote located catch can that is vented. That will relocate the mess to the top of the catch can.