Actually that did happen to me, but only to some of my zoos so I did not try to figure out the problem and just gave up on them.
The one thing I would suggest is the problem might be that you are using user objects that weren't updated for AA. If those objects are in the zoo it might make the program crash when called up. For example I had a problem after I updated to AA that whenever I placed a Shetland Pony the whole game would crash, and it was because the pony wasn't supported for AA. The only solution for that (that I can think of) would be to do what Budgielover said and uninstall AA, and remove those objects from the zoos.
The other thing you could try is to see if someone else who has AA can open one of your zoos. If they can, it might be that the game is messed up, as opposed to the saved game files. Then you might need to uninstall and reinstall everything to fix the problem.