I think we can agree that is counter-intuitive but it worked (for the most part). It showed the couldn't load message so I had Certify The Web deploy the file again. Though there was only one file in the folder SM showed 2 certificates. One it could load and one with the error message displayed.
No amount of messing with the check boxes permitted me to remove the bogus one. So I deleted the files intending to copy them once again.
I thought I would try to remove the bogus message from SM and I pressed the Choose File button on a dialog having entered no password. I now have a spinner running with a Next button visible but everything is disabled. If a required input is missing I would have thought it wouldn't proceed. The site is pretty much hosed and disabled though my browser will step back. I just exited out of the site.
Ok back in and it shows no certificates which is expected. Deployed the cert and it shows 1 cert and it is active so I think all is well again.
Thanks for the assistance. I understand very well how making things obvious for every user is an impossible task but this was a bit more mysterious than it probably needed to be.
Thanks again.