Scroll ran into this issue too. We changed the default turret loadout on a few ships, but the MediaVPs overrode them, so we had to override them again. FSU's original intention was to change the various Terran Turrets to Vasudan Turrets for Vasudan ship classes, but this can have unexpected side effects.
I developed a tool for Scroll to print out the weapons assigned to turrets, among other information. This helped troubleshoot whether the loaded game data differed from what the mod expected. If there's interest, I can add this as an FSO feature, similar to -weaponspew and other debug logging tools.