The best hint we got, and one of the few bits of real character exploration for her that we got once SkrullJess was replaced with RealJess, was during the Fearless tie-ins in the Avengers books. During those talking heads issues that everybody but me hated, there was some statement from Carol about Jessica "going to a dark place" when she was alone.
I appreciated the statements surrounding that as it was some recognition that yes, there IS something going on with her and it is not bright, shiny, nor happy. The real frustration for me was the "resolution" of this. "Ok! She punched the Hulk and kissed Clint Barton. All better now!"
That's why I really wish her solo book had survived. I actually do believe Bendis would have done some interesting exploration of her mindset and some of the darkness that surrounds her, he just never made room for that elsewhere.