No. It's not a problem of your storage's HCA firmware 2.9.1000.
If your Hypervisor is ESXi 5.5 or above, i'll make firmware 2.9.1200 for MHGH28 or MHGH29 CX-1 families.
I was confirmed successfully before that old HCA.
I'm so sorry for my late reply, because I was very busy for my works...:)
I'll link to you firmware 2.9.1200 for MHGH28 CX-1 HCA.
This firmware can support Intel vt-d enabled system...:)