Text Recognition with docs that have searchable bates number in footer.

In the older versions of Acrobat, we could run text recognition on documents that had headers and footers (headers from courts) (footers like bates numbers) that were searchable.  Adobe XI is not allowing us to run recognition on documents that have a searchable bates number at the bottom now.  Is there a setting someplace we can change so we can do this before we have to move to a different product?