Client certificate authentication and IIS 6

I have an IIS 6 web server which I want to secure with SSL and client authentication. Using locally generated certificates (MS cert server) it fully works in development with IIS checking for client certificates and rejecting if not in the rule set.

We then purchased some SSL/Client certificates from Comodo and are trying to use them. The SSL part works fine but IIS is rejecting the client when conecting using the purchased certificate. The certificate propereties state in the enhanced key that it can be used for server and client authentication.

Any ideas why they don’t work, should SSL certificates be able to work as client authentication certificates?