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After further troubleshooting, I believe the errors were being logged whenever a database was accessed which had agents signed by the server previous to a certifier rollover.
I ultimately eliminated the errors being logged by reinstalling Domino and starting fresh with a new certifier and Domino directory. Databases restored from backup (including especially mail databases) that had agents signed by the server needed to be re-signed. During the re-signing process, certificate errors were logged in the server log "Error processing certificate created by /org for server/org" but once the process was finished, the Notes clients no longer logged any errors.
Feedback response number BERNAPNSMC created by ~Manny Fezrezenakoi on 07/27/2017