I've tried all sorts of different things to try and cure the problem but reading your reply prompted me to try something else.
I opened Pages and dragged the window above the dock then, instead of using the red button to close it, I quit it from the drop down menu. Next time I opened it the window was above the dock! Trying it the other way and just hitting the red button until I next needed it resulted in the window behind the dock again.
The moral to this issue is to always Quit the app and not use the red button which just closes the window.
I assume this is the way it is intended?
Thanks for pushing me in the right direction.