I also seem to recall times where she internally questioned his actions/behavior but doesn't follow up, though I can't recall any specifics--been a while since I read them. It could argued that she was busy/pre-occupied, but that only goes so far. As for her believing in the inherent goodness of others a) he's betrayed her before and b) she's willing to question Cole's trust-worthiness at one point, who she's known for years and loves, yet she's going to give Walter the benefit of the doubt?
I dunno, it all just seemed a bit off to me.