Looks like you have your answer on the bead.
Picture #1 is a great demonstration of what happens when the mating surfaces aren't thoroughly painted before assembly. Once it rains on the car, water is sucked into the seam by capillary action and it stays wet for weeks. The beading fabric helps hold the moisture, it soaks through any surfacing primer and begins rusting almost immediatly.
The presence of silicone sealer will intensify this rusting process by 5X...
It appears the windshield frame suffered a similiar fate.
I can see you're in the primer stage and it looks great!
I like to sandblast these hidden edges and grooves and seal with epoxy primer, then paint, before assembly and final paint.