Have you registered your Cert with the Host?
Inside the BizTalk Admin, right click on the Host (not the instance). You can assign cert there.
Also I have working with X509 certs with, um, another version of BizTalk. I was unable to read from CurrentUser and had to use LocaComputer as a store. Not sure why, but I think it was a permissions problem.
Sorry I can’t be of more help.