Hi Andreas,
Please have a look at the section "Basic Password vs Ticket Authentication" in the release notes for your version (in the documentation).
This basically boils down to the following issue:
There are two primary authentication systems on Netweaver, container based authentication, and programmatic authentication. SAP CPS uses container based authentication and I assume your certificate login uses programmatic auth. You can configure NetWeaver to use login tickets which should solve your problem. Please consult SAP support for the configuration instructions.
The instructions can be found here: http://help.sap.com/saphelp_nw73/helpdata/en/4d/a5ddc832211dcde10000000a42189c/content.htm
Thanks,
HP