I had another look at this today... still a mystery.

On the PSE three of the lines are common and labeled A,B and C. Using the mity vac I can lock the left and right rear door when pulling a vacuum on lines A and C. Both hold and show no signs of a leak however, line C leaks down and does not lock the trunk or the gas flap.

Hmm... Both the trunk and gas flap lock and unlock as intended when using the key fob.
Stumped.