The Intermediate CA problem
From OpenCA Labs WiKi
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Description
After creating a Self Signed CA Certificate, when you import it in Internet Explorer, it does not recognize the CA certificate as a Root CA but only as an Intermediate CA.
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Solution
This is an issue with IE7. To fix the problem you should import the certificate again but on the certificate store window of the wizard, do not choose the automatic option - choose the 2nd option, browse, and place the certificate in the Trusted Root CA store. (Depending on why you are trusting the root, you may also want to choose "show physical stores" option in the browse window and put into Local Computer Store of Trusted CA or Registry - depending on why you are trusting it). Alternatively you can run the Certificates MMC and import the certificate.

