After deciding the motherboard was fine I swapped it out into a different tfx sff case with a bigger psu so that i could fit a discrete gpu and have had no issues with it what so ever.
I moved the pegatron board that was in my old case into the esprimo case, this board has always been pretty reliable but since fitting it into the fujitsu case I have started having an issue booting reliably so you may be right about my theory being off track.
When starting from a cold boot the pc boots fine but if I hit restart from windows the boot device order changes, the hdd still shows as being detected during post though with the quiet boot option off, I keep having to go back into bios and reset the boot order during restarts.
This pegatron will automatically try to emulate usb devices as hdd or fdd based on size (below 530mb ffd above hdd) but even my empty usb multi flash card reader is given priority over the hdd, my guess is that you are right about the psu being an issue and somehow during a restart the hdd is not initialising/ powering up properly leaving me stuck on the boot device search screen (black with blinking cursor).
Unlike the fujitsu board I do not have the option to exclude specific devices from the boot order, they are redetected at every boot but somehow the hdd is just losing it's priority during restarts, this may well be an issue with the psu not powering the drives properly.
The thing that threw me with this pc from the start was the fact that the psu, heatsink and motherboard looked brand new, no dust whatsoever on/in any of them, if it wasn't for the odd ram sticks and a few scratches to the case and the coa being missing I would have guessed it was new old stock, but now I am starting to think it had suffered a booting issue from new and had been scavenged for parts.
Either way I can't complain for £35 I have a decent ddr3 motherboard, an e5800 cpu and 250gb Seagate hdd to play with, If I can find a way to fit a standard tfx psu into the fujistu case I might keep that one too if not I will just buy another case for the pegatron board.