I don't think I would put a pee pad in her crate as I think that would only reinforce her going potty in there. I imagine it is just the change with the baby. We have a weiner dog that was my dog and loved the fact that I had such a horrible pregnancy. He was by my side while I was laid up morning through night. But when the baby came he disowned me like yesterday's news. That was 8 years ago and he still only puts up with me when I am giving treats to my two yorkies!!!
I think it'll just take time. And I am sure somebody here will have a GREAT suggestion. I wish you the best of luck as I can only imagine how trying this must be when you are already sleep deprived with the new baby (and congrats on that BTW).
Peggy, Monkey & Maddie