Humm, I think I found the problem with the end of the dark area. When you save Sylph and exit out....it was supposed to play a scripted event right when entering the hub again. That was where the next hub tag was. So it should have been saving, but just not properly advancing the tag to the next hub. I think I got it now.
Programmer says he hasn't touched the ability binding change since the last version, so not too sure on that one. Trying to track it down :D