If you want to use Smart Card authentication in a with ThinApp virtualized Internet Explorer there are a few steps to think about. VMware has published a new knowledge base article which does explain what to do, to support this type of authentication within the virtualized application package.

Link: http://kb.vmware.com/selfservice/search.do?cmd=displayKC&docType=kc&externalId=2007858&sliceId=2&docTypeID=DT_KB_1_1&dialogID=643264355&stateId=1%200%20643270670

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