If you see a change in manifold pessure when adjusting the mixture, you've chaned the engine RPM to do so. If the RPM stays constant the the manifold pressure stays constant.
When the mixture is enriched the RPM drops. The idle speed is then adjusted up by opening the throttle plate a little. So you end up with both engines at the same RPM but at different manifold pressures. Works every time. The split in MP will decrease as the throttles are opened further and the main metering system comes into play and the idle system becomes irrelevant. Can't say for sure at what RPM this will happen.
Since it's cheap and easy and a likely cause, I'd check the idle mixture first.
As for the prop low pitch stop, it will usually give a steady split in MP until the governors move the blades off the stop to a coarser pitch to control RPM. So you should see the MP split go away at TO RPM if that's the problem.