I can't help you guys, just to say - two 9361 (bbu, cachecade, etc) are working fine, I tried DELL and IBM ones, mixed or both DELL, no problems at all.
The only change from default settings is that I have disabled BIOS on the cards because I don't need to boot from RAID and it's bit faster. Also, they can be configured thru UEFI bios (bottom of advanced page). If more than one 3961 is installed, UEFI bios nicely lists all of them in advanced page and I can select which one to configure IBM 5210 or DELLs 9361.
If it matters my mobo is ASUS Z10PE-D16 WS (dual socket). So problem looks more like mobo configuration than controller issue. Silly to mention but any OEM card can be flashed with firmware from broadcom, maybe they fixed issue by the time? Have you tried ? I flashed IBM and DELL cards with one from broadcom, they work well.