We have someone stopping by today between 2 p.m. and 5 p.m. to investigate the mold growth in our windows. Since I posted the first pictures, we noticed the window to the right of our bed also has the first signs of mold spores, so I'm thinking they did something wrong in installing in that particular location. We've looked at the rest of the house and everything seems on the up and up. Keep your fingers crossed that it's as simple as getting new panes installed and they don't have to rip them out of the wall. That'd suck.
UPDATE: New glass panes are being ordered and they should arrive in the next 2-3 weeks. Very easy process so far.