Fixed this problem if anyone else has the same setup as me as it was very odd.
I found that if with the vehicle ignition on and engine running I toggled my 3 way switch to off (i set up the standard perm on, ign on or off 3 way switch to feed my power supply IGN wire), then m2 ATX would correctly after 30 seconds or so send the signal to the PC which would hibernate correctly. If however I left the toggle switch in "ignition" mode and just shut off the ignition at the key (stopped engine), the ATX power supply would just cut the power to the PC and it would be instant off (no shut down or hibernate) as if I had pulled the power lead out of the back of my home PC.
I had not realised this was happening because a) the screen would go off and b) when i restarted, I was getting the windows resume message making me assume the system had actually hibernated. So the problem was that it seemed to be resuming but no programs were running.
It appear that the problem was that I naively had the 12V power (continuous) to M2 ATX supplied from my secondary leisure battery but was using the 12V ignition supply from main battery with common earth of car body and this disparity in power sources was causing the issue ( i think).
To fix it, I just used the 12v ignition supply to switch a relay in the end and sorted it that way.. I think the PC was showing as resuming even though it had been just powered off was because the hiberfile remained on the system (might be wrong though)..
for info, my install is in a VW T5 van so I have a secondary battery fitted to power the auxiliary stuff and had wanted the car pc to be run off that so that in the event of a ATX power supply problem / PC locking up on hibernate, it would not drain down my main cranking battery..