In playing around I've also confirmed that the problem can be recreated if the monitor connected to the HDMI port is turned off. After approx 5 seconds the monitor on the VGA port flashes and is given primary display. When the monitor is turned back on it no longer has any signal and the computer also does not recognise any connection on the DVI port.
This seems to be either a BIOS issue, and thus needing a programming update, or a chip based problem on the motherboard requiring a motherboard replacement.
Your thoughts on this greatly welcomed. We do not have other motherboards of this type in stock to test. That said given the numbers of other users seemingly facing this issue it would seem that the issue is most likely BIOS related as the issue can be easily resolved. That said although the solution is easy it is incredibly annoying to have to reboot your computer every time the monitor is turned off manually or the PC places the monitor into sleep mode etc.