Site in Azure Websites fails processing of X509Certificate2

I guess you found a workaround, but if others are struggling with this, I found the answer to this in another SO question:

How can constructing an X509Certificate2 from a PKCS#12 byte array throw CryptographicException("The system cannot find the file specified.")?

The magic is specifying the X509KeyStorageFlags storage flags. Example:

var myCertificae = new X509Certificate2(
    certificateData,
    securePasswordString,
    X509KeyStorageFlags.MachineKeySet | 
    X509KeyStorageFlags.PersistKeySet | 
    X509KeyStorageFlags.Exportable);

Azure Websites now has native support for installing certificates to the certificate store. Have you given that a shot?

Details here: http://azure.microsoft.com/blog/2014/10/27/using-certificates-in-azure-websites-applications/