Relative signal strength
You say you heard a sig on 144.39 that was stronger than your tracker in the same building with the scanner? That is suspicious. I'm still guessing you have a driver stage putting out a few mW into a blown final which is letting some micro watts pass to the antenna. Audible at ten feet inside the hangar but not at ten miles to the digipeater. Can you measure the current the tracker draws when it keys up?
Keep investigating. Whatever it is is fixable.