Can you try installing ESXi 5.0 (or 5.5)? I had this controller and I remember it was detected with all arrays. I did not have to do anything special during installation. I do not have it anymore so I can not test if ESXi 6.0 can detect it (and arrays)...
btw when you jumpt to controller-bios (webios or how it is called) during boot-up, do you see arrays? Are they initialized?