If you have the “Force rewrite rules” checkbox ticked then try unticking it. There appears to be a few bugs with this some some installations and I just fixed a site with a similar problem doing just that.
This was a great fix for the problem I was having. I was having the same issue as OP, and had changed my header.php to have the titles push through, but left the force box ticked. Unchecking it has corrected my issue entirely! Thank you!
