I posted this question to the forums at vbaexpress.com and someone was kind enough to help me with the following advice.
"First of all be aware that you may have problems with macro security if you use vba. On many institution PCs vba is disabled
You need to run the 'I am already saved' code at the end of your show.
Press f11 to get to the vb editor
In this INSERT > Module
copy and paste in this code
VBA:
Sub Iamsaved()
ActivePresentation.Saved = msoTrue
SlideShowWindows(1).View.Quit
End Sub
If you have a next slide or end show button on the last slide select it and change the action to RUN Macro"
I had to play around with it quite a bit it worked in the end. Hopefully this will help out someone in the future with the same problem!