Hmm, I've never run across this myself. But just thinking it through it would make sense that somewhere in the system there is a clog that's blocking flow to the pump, which is causing a section to be under vacuum.
I guess work your way out from the pump and find what is and isn't under vacuum and hopefully that will help point to where the blockage actually is.
I've heard of using tranny fluid when you do an oil change to get rid of gunk built up in your engine. Not sure if that would be appropriate in this situation, but the concept might work? A detergent or some sort of plumbing cleaner run through the system to get rid of anything built up.
Short of that, I'm at a loss.