I figured he always knew but chose to look the other way, like when he asked Padme if Anakin was the father.

Yeah, I've always kind of thought that as well. I just like this, I think it's funny. Plus, I ship Anakin and Padme so hard! I fangirl whenever I see them!

I've also figured that Obi-Wan knew that Anakin was in immense pain, and he clearly knew that Anakin loved her, and he knew that if she was with him, his pain would be less, and I get the distinct feeling that Obi-Wan hated seeing Anakin in pain.