Some lo's just don't respond well to walk in/walk out and seem to be better with a more "mommy involving" sleep trainging technique, which is what you're doing and is called Gradual Withdrawal. A sep, anxiety spurt is usually held back within 2 weeks or so if you handle it right (which is what you're doing). You've ruled out teething, illness, but what about lights in the room (is it too dark, too light?), temperature or comfort (she might be umconfortable in her pj's... that happened to me once, ds grew a lot in aweek and i couldn't figure out why he would refuse to go down... switches pj's and that was it!)..
If everything is ok, then keep at the gradual withdrawal working your way out of the room moving your quilt a bit far away from her crib every 3rd day. As long as you reassure her you're there for her (which is what you're doing) she'll be fine soon.
As for the night wakings, do the same, whenever she wakes, stay in the room to help her soothe and then walk away. If she's too distressed go back to your quilt and eventually you'll be able to walk away.
HTH!