Ok, so I've done some testing of the new V1.4 Multi for those of us with Namco Noir cabs or cabinets using the NAVJ2 IO boards. Here's what I've found.
On a single player Namco Noir Cab not linked
These games have all got the dreaded coin error:
-KOF Ultimate Match
-KOF XIII
-KOF XIII Climax
-Senko no Rondo Duo (the fault was in Japanese but I'm assuming its the same)
-SFIV
-SFIVAE
-SFIVAEE
-SSFIVAE 2012
-Trouble Witches
When Linked to a second cabinet
-The multi defaults to P2 cabinet for control and P1 controls don't work even after resetting out of a game as they did in the previous version.
-With the P2 cabinet linked you no longer have the coin errors that are present with a single cabinet however there is a bunch of new issues.
Chaos Breaker - Players reversed
Gigawing Generations - IO error then reboots
Homura - boots no controls at all
Raiden III, III Export and IV - P2 cabinet controls act as Player 1 and no P1 cabinet controls at all
Shikigami no Shiro III - doesn't boot at all, just freezes
Spica Adventures - same as Raiden games
SFIV - no longer boots "JVS ERROR 0005: Connection out of spec"
SFIVAE - as above
Trouble Witches - same as Raiden games
Games not mentioned worked without any noticeable issues in the respective cabinet configurations.
@Niko if you would like me to do anymore specific testing let me know. Hope this helps a bit. I haven't found any info on the Namco IO cards anywhere so I will try asking Namco support for some info. I don't like my chances though. There are a few dip switches that must do something.