I'm sorry to hear of this latest development. I am guessing that you already know what you need to do, but I'll let you hear it from me.
You've been at this a while. She acknowledges that you have had some good times. She knows how you feel. Something is still causing her to want to pull away.
It's time to let her without any (and I mean ANY) resistance from you. No rationales, no arguments, no hurt feelings.
If she hasn't already moved out, help her do it immediately.
Time for Tough Love (get Dobson's book now if you don't have it and follow it to the "T").
And have faith. If it's meant to work out, it will, but as sure as I'm typing to you, you can be sure it will never happen on your timetable...only her's, and she's made up her mind for now.