I sent a document out to be signed. It was signed using a certificate. Now I want to counter sign. however, when I select to sign with a certificate it will not allow me to do so. it is as if I am locked out of my own document.
You are locked out of your own document if they chose to lock it (or you set it up to be locked). There is no "oh it's you, you can sign because it's your document" feature.
You should have added multiple signature fields before sending out the file, and set them to not lock each other when signed.
It's possible you can't do it now since the file was not set up correctly for this kind of workflow.