I have the following code. I am always getting a false when looking for the private key.

CertificateStore certStore = new CertificateStore(CertificateStore.MyStore);
Certificate cert = certStore.FindCertificateBySubjectString("TEST");
bool boo = cert.HasPrivateKey();
string name = cert.GetIssuerName();

Are you sure that the certificate in the store is associated with a private key? Does your user have the appropriate permissions to access the private key?