Here is the code to add a pfx to the Cert store.
X509Store store = new X509Store( StoreName.My, StoreLocation.LocalMachine ); store.Open( OpenFlags.ReadWrite
This is the solution I found for windows server 2008 if anyone was interested: http://technet.microsoft.com/en-us/library/ee662329.aspx
Basically, I had to grant permissions to the service that needs to access the certificate using the MMC tool. Works like a charm.