We're fine. Although I do hope that next time you pick an instant to have your computer hardware break it doesn't coincide with some of us experiencing the exact same symptoms from a kernel update at that exact same time...
At long last I have found the culprit. I have been waiting for a USB 3.0 front panel adaptor to arrive to put in the slot that my Floppy sits. I already have a Pcie USB powered adaptor fitted with a socket for extending the USB 3.0 slots to the front. I also had a USB 3.0 two port docking station connected to one of the USB 3.0 ports on the Pcie adapter.
I stripped the PC down and fitted the front ports and connected it to the pcie adaptor. I then thoroughly checked all the connections to the two internal drives, plus that the RAM sticks were properly seated. Then before I boxed up I then booted up and I rebooted and all was fine. I then shutdown via the OS and it shutdown perfectly; I assumed that it must have been attributed to one the things I checked on.
Then I boxed everything up, connected all the other stuff but when I booted up nothing was showing on the screen. I fiddled with the HDMI connector and then I unplugged the USB 3.0 lead from the docking station to the rear USB 3.0 port. Then everything became alive and it booted up. I shutdown again and same problem. So this time I pulled out the lead from the USB Dock St to the rear USB port. After another reboot I then shutdown and it closed instantly! I then connected the dock st to a standard USB (2.0) port and all was working fine.
So the issue is with this older machine I cannot have that docking station hooked up to the USB 3.0 port. Obviously being an older system it does not recognise USB 3.0 ports in DOS mode. It is fine when I am in Linux the ports are seen. On reflection I should have realised this earlier as when I had my keyboard plugged into a USB 3.0 port it was not recognised. Do not understand why though when a USB 3.0 accessory is connected to one of the USB ports it prevents the machine from shutting down properly. Just wonder if there is a workaround for this problem.