I know this has been a problem for many MSFS users, but the underlying reason is not clear. In my own experience with MSFS flying many different aircraft, it has never happened to me - for other users it, it seems to happen on every flight with Live Weather active. On a recent Avsim post, a user flying the default Baron always saw the aircraft level at the 29.92 pressure altitude corresponding to his altitude selection. I flew the same aircraft, at the same location, and it worked perfectly every time. It worked whether I synced the altimeter by manually dialing in the current altimeter setting - or whether I auto-set it with the B key.
Yet, for the other guy, same airplane, same airport, it was definitely not working correctly - he made a video showing the effect.
A definite mystery.