I hope you have already received an answer to your questions via another method (it has been three weeks), but just in case, I'll try to help.
I'll answer the last question first. When a VirtualConnect module is attached to a switch operating in NPIV mode, the logins from the hosts (blades) are passed through the VC module to the core switch, in this case, the 9140. The process is pretty straightforward. When the VC link comes up, it sends a Fabric Login (FLOGI) to the core switch. When the hosts come up, they send a FLOGI to the VC module, and the VC module sends this login through to the core switch using the FDISC command. The core switch will now see multiple logins on the same physical port. As an example, if the 9140 VSAN was domain ID 0x01, you might have a host login with the FCID of 0x010001, then another with 0x010002, and so on.
In this way, the VC module is somewhat transparent to the core switches... all the core sees are multiple logins on the same physical port. That is why you do not see the VC modules as devices, because they are not operating as a true FC switch. For reference, a Brocade switch operating in Access Gateway mode, or a Cisco switch acting in NPV mode work exactly the same way.
As for the third VC module not coming up, that is a tough one. If the third module is connected to the same switch(es) as the other two, then I will assume the 9140 is configured properly (NPIV enabled). One thing to check is what port VSAN the third switch is configured for. All of the hosts that login through the 3rd VC module will login into the VSAN where the VC module is plugged into. So if the 3rd VC is plugged into port 3, and port 3 is in VSAN 10, then all of those hosts will only be able to see targets that are also in VSAN 10. And that brings me to the last thing to check. Even if the targets and host ports are in the same VSAN, you will then have to zone those hosts to the targets. In fabric manager, from the Physical Attributes pane on the left, expand End Devices, then click on hosts. For each uplink from the HP VC modules, you should see multiple logins from the hosts on the same FC interface of the 9140. Pay particular attention to the FC interface where the 3rd VC Module is connected. Do you see multiple login's on that interface? If so, then everything is working as designed. In this case, it is probably just a matter of zoning those initiators with the right targets. If not, then the logins from the hosts aren't making it to the 9140.
