That is what I tried as well but the Running Configuration these lines;
crypto pki certificate chain TP-self-signed-########
+ certificate self-signed 01</p><p> 123412354 etc.. (rest of the certificate)</p><p></p><p>The Startup Configuration has the following lines.</p><p> crypto pki certificate chain TP-self-signed-#######</p><p> certificate self-signed 01 nvram:IOS-Self-Sign#1.cer+
As far I can tell since the certificate is not displayed in the Startup config I get a Conflict, which is really not a conflict.
Thanks for the suggestion though, I had previously run an Excute Script with other changes and made sure a "write memory" statement was in place at the end of the script. This aliviated some but not all of the conflicts.
I have found on cisco's website that what I am seeing is considered a feature in new IOSes. The certificate is actually stored in nvram and is referenced to the running config to be displayed. Bryan does a better explenation in the following forum.