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Looks like Carol Bailey wrote up a great post on a couple issues relating to native mode certificate selection. If you're seeing either of these then you might want to check out the link below:
A couple of issues recently came to our attention from the TechNet forums with regard to native mode certificate selection when there is more than one available certificate that could be used:
For all the details see http://blogs.technet.com/configmgrteam/archive/2009/12/15/known-issue-logging-information-for-native-mode-certificate-selection.aspx.
J.C. Hornbeck | System Center Knowledge Engineer