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Here are some other threads discussing the problem: : Import SSL certificates into Domino : View / Export Private Key in keyfile.kyr
IBM used to have a technote that included the correct ikeyman program and some instructions, but for some reason they have deleted it. It was titled "How to export the private key from a Domino keyfile by using IKEYMAN" (#1308138)", and was at this url: http://www.ibm.com/support/docview.wss?uid=swg21308138