Hello again Phill,
You are spot on as it was the problems that you had with the new IDE DVD drive that I was thinking of, glad you remembered 
Yes, glad we sorted that out! 
The behaviour is odd because it has only just begun when you have had the clone on the second HDD for so long, it is what should have happened from the outset though as you effectively have two identical working OS ready to load, if it doesn't bother you having to select the primary OS every time you could leave things as they are, the only alternative is to disable the cloned HDD in the BIOS.
Yes, this is very odd. My clone was first created - with your assistance - back in 2014. We tried then to just change the drive letters - but in the end the only way to do it was to swap the leads over (edited). It wouldn't do to disable the cloned HDD in the BIOS as there is another partition on the same drive on which I store all my data, so I need access to the drive.
I believe the computer set-up has not just been like that since 2014 though...... It was only after creating the clone and seeing how it appeared from the other drive that I realised that it has probably been like that since 2006! The computer actually came with an exact copy of the OS on the second drive - so that without ever being aware of it, I could have at any time since we acquired the computer in early 2006 have swapped the leads over and booted from the other drive. So I think that this has changed something that has always existed. 
NB: Looks like the AIO tool fixed something that you may not have wanted it to
I think you are wrong there. This did not happen as a result of running the AIO tool. It was when I inserted the Windows 7 CD that the problem arose. Going back to message #25, I said: -
There is one odd thing that happened when running the DVD though. Right at the beginning it told me: 'Windows found problems with your computer's startup options. Do you want to apply repairs and restart your computer?'. When I agreed to do this, I was not sure what to do on the screen which followed, so exited with the intention of trying again later. Now though, whenever I start the computer I get the following screen: -
It was immediately after that that the boot manager came up (though I did not even realise what had happened and just clicked out of it at first) and has done ever since. It seems that Windows just took it upon itself to decide that the way this computer has been set up for 11 years was wrong and that it needed changing! 
I am still having problems with the services btw: any further thoughts on that? I think you mentioned we might have to edit the registry?
Thanks again for all your help,
Chris.
Edited by Channeal, 27 May 2017 - 05:22 AM.