Odd city and region problems

[Koetsu]

This is the most recent city I've made and it turned out surprisingly successful.
http://i.imgur.com/AxyxTAw.jpg?1
However, I noticed that some things didn't behave the way they're supposed to. First, I noticed that the environment value seems to have permanently spiked down since I started the map. It makes no sense at all since on past maps, it has never been a problem. Also, I somehow managed de-unlock the University, despite that I've long-exceeded the requirements. On buildings that have random quirks it keeps track of, many of them have a 0. Pigeon nests, stadium sponsorships, the zoo. In my experience, that's never happened before. And finally, when I ran and saved an old city from before, the thumbnail disappeared.

The most recent change I've made is that I installed and started using the quick launcher. I've had some NAM for a while but I don't know how any of that could explain these oddities.

Well now, I think the bigger concern is how I was once offered the University, then de-unlocked it. Can I save edit that back in or something?