Pull the vacuum port off the MTX and turn the ignition on. Does it still read 3"Hg?
If so i'd say there is something wrong with your Vac sensor. The sensors are usually very accurate and with it at atmosphere should read 00"Hg.
You could still have vacuum captured somehow, perhaps a solenoid is closing when you turn off your key and it is causing a vacuum lock. Where is it tapped into the manifold also?