If you email me your zipped save I can take a look at it, but can't think of anything to try to fix it. A new game works, so the problem is probably be something in that save itself.

I'll check my save for the active teleporters (I think I got all of them in Rivertown and Verdistis)...
Yes, I had activated all 12 teleporter pads in Rivertown, and the one in the Verdistis park. I had not activated the one on the Verdistis sewer, or any of the ones in the Dark Forest.