Jeff, Trapt gave you excellent advice. She obviously felt that she was feeling entirely too comfortable w/you and felt that she needed to distance herself a bit. She's not ready to recommit to the relationship or you just yet. What do you do? Distance yourself, keep busy and put your expectations back down to zero. Keep repeating...she's a roommate over and over again. She's got to work these things out within herself. Yes, you've been doing a great job, but she's feeling a tad pressured by all of what you've been doing. I know, most women would be thrilled to have you helping out, but she's still not quite there yet to really recommit.
Jeff, it's a dance, follow her lead. Okay?
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.