If anyone encounters this again it turns out that Supermicro are aware of the issue:
https://www.supermicro.com/support/faqs/faq.cfm?faq=21114
Question
I am having problems booting X8DTN+ motherboard from a USB . I have a PCIe raid card and a PCIe HBA card on the board. If both cards are installed, it will not boot to USB. However if I remove one of the cards (doesn’t matter which) it will boot to USB. I have tried using different slots with the same result.
Answer
Please disable the OpROM for the card that does not have the OS. Say HBA is used for data drive, then disable the OpROM for that PCI-e slot. Disable under BIOS >> Advance >> PCI/PnP Configuration >> Slot# PCI-E Option ROM >> disable the slot which HBA is installed in.