Lionel and I have been chatting this morning about this. We both expect MySQL Compare to automatically ignore schema names. We are aware that the highlighting in the difference pane shows the schema names as different but that is not considered different by the product engine.
I really would like to help figure out what the problem is. Can you please email us at firstname.lastname@example.org
, perhaps with an example of the schema in which you see this problem and we can get to the bottom of it for you.