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You should check your wget version. I had the same problem with older versions of wget (< 1.15).
gpg-agent and most probably ssh-agent, too, doesn't care what the keys belong to. The keys are identified by their keygrip (the fingerprint of the pure key material whereas e.g. an OpenPGP fingerprint is over the key material and some additional data like the creation date). You can enable / increase the logging in the config file ~/.gnupg/gpg-agent.conf. ...
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