I have basically obscured the blank background canvas with an invisible button, set the function of it to "none".
So now the user can click away but it wont advance any slides unless they click on the actual buttons i have set up
May I translate this to what I understand now? The click boxes were not pausing the slide, you never told about buttons because buttons DO have the option to disallow Continue Playing the Project when using a simple action.
You did use a workflow which I described in an old post about the Timeline, where you put a Shape button (another button cannot be used) on the Blank master slide. If you keep the default setting, that button will pause each slide, based on the Blank master slide at its last frame, whatever the duration of that slide. Since the PPT slides do use the Blank master slide, this option will work.
Here is a link to that old post:
http://blog.lilybiri.com/easy-timeline-tweaks
It is Tip 1, applied in this case not to the Main master slide, but to the Blank daughter master slide.