I'm Dr. Jackie, a communication researcher/professor and relationship expert. And I wil try to answer this to help you. However, there may be several possibilities. Since I do not know your partner and obviously have never talked to her, I'll try to lay out several options with some details that may help you narrow it down to what specifically may be going on.
As with almost anyone contemplating a wedding, surely she knows/knew at the time you left her to plan a guest list that you care very deeply for her, even if you did tell her in a silly way with your lips forming "I love you" just like with "elephant juice" or "olive juice."
So at first she was excited because this is something that many women dream about when they are young girls. And when the proposal actually happens, it is truly a dream come true. Now here is where there a few different possibilities
First (and I think this is the least likely) is that she was comfortable with you as a roommate/best friend/activity partner. Yet as do most girls growing up, one major life goal was to get married. So while she is in love with the idea of being married, her feelings for you have been more platonic, more friendship for over a decade. So after she said, "Yes," she became confused about her feelings and finally was honest with herself, realizing that maybe in the beginning she was more romantically attracted to you but after so long it evolved into a very close friendship.
A second possibiliity is that she is torn apart because she is not sure if you are in love with her or if you love her as a very close companion. Unless the culture in your country is very different (and I confess not knowing much about British or any other cultural norms), 11 years is on the long side to be involved without being married or establishing some type of "life partnership" or whatever other label you want to attach. So it is possible that she thinks since you didn't voice, "I love you," maybe she thinks it may be more of a special friendship feeling ON YOUR END versus the first possibility of thinking that way herself.
A third possibilitiy (and the one I tend to favor at this point although I know I don't have all the information really to make a more informed opinion) is that she has been depressed or has something like a mood disorder/bipolar disorder. This would explain her saying that she is unhappy but not knowing why. In other words, it might not be about you/your relationship nearly as much as it is about something going on inside herself--maybe she has a chemical imbalance or something else that is affecting the chemical make-up in her mind. A medical doctor should be able to diagnose this.
Please let me know if this helps--or at least gives you a place to start. I'm more than willing to keep chatting either through this Q&A forum or via phone or SKYPE. I'll send you my contact information through our JA form if you ever want to do that.
Please let me know. Take good care,