When I examine the Score Comparison page in the Ledger and hover over Mil. Rating I show a red negative rating for Fort Maintenance. When I develop the province the negative number grows.
Pretty sure this is it:
You need a certain fort level per dev point to achieve the max Army Tradition. I think the amount is the same for the score.
To explain it differently: The Fort Maintenance component for your Military Score is probably directly related to the Fort Maintenance component of Army Tradition. For Army Tradition, you need 1 active, current-tech fort per 50 development.
When you developed the fort province, you increase your total development without increasing the total number of forts (i.e. forts/development decreases), causing your score to decrease.
Instead, to increase your military score, you need to build more forts, keep them active, and update any old forts. While you might have a valid reason for this (is this the score used for contesting inheritance?) , most people (myself included) think this is a waste of ducats (in single-player, at least).