Windows includes a number of root certificates from Certifications Authorities (CAs): StartSSL, Thawte, Verisign, etc ...
To view the listed CAs, click on Trusted Root Certifications Authorities > Certificates:

Make sure your Certification Authority (CA) are listed.
If your CA is not listed, you may add it.
Let us take the example of CAcert.org.
To add CAcert.org to the list of registered CAs, follow these steps:
Download CAcert Class3 root certificate:
http://www.cacert.org/certs/class3.crt
Double-click on the certificate and import it:

Click next, and select the default location:


Validate:

Now you should see CAcert.org root certificate in your list:

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