hottrout - 9:10 am on Feb 2, 2012 (gmt 0)
Actually I read all of the portions of Jim's old thread reply. I might not understand it entirely but I did read it.
The malformed links are not being created on my site. Google webmaster tools is reporting them as 404's coming in from other sites. For a reason outside of my control their browser is seeing the link and replacing the ? and = with the replacement %code.
Am I wrong in thinking that there is nothing I can do from my side? A full check confirms that my site produces the URLs correctly with the ? and =.