Detailed investigation by our EMC guy showed that the Cisco SAN switches were talking FC-AL (Arbitrated loop), for some reason. After shutting down the second port/path on the SAN switch, the installation CD only saw one set of devices and was no longer confused by all the LUNs that seems to be the same (they were!).
Lesson learned: limit your variables during installation and only use one SAN path. Activate the second path during post installation (you need drivers or software anyway). Powerpath in my case.