I haven't heard of this problem before. Offhand, I would say it is a problem somewhere else other than the certificate. However, you could try to uninstall the certificate by manually deleting the certificate db tables and then deleting the files. If you can get to your admin block, try turning debugging on to see if you get any error messages of where the problem is.
If this is a working site, you need to be sure to back up your db. Then, you can try updating again to the latest 1.9 version of moodle. It may be that you have a version with a problem.
Custom certificate (plugin)
Instalation of Certificates doesn´t concludes
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