I found a working solution of calling a macro from VBScript.
Here is the code that does what I need. Which is to open the PPT file and perform the macro. I don't get prompted to update links.
Unfortunately PPT must open to perform the macro but I'll just have the macro close PPT once it's finished or have it call on another macro to close it.
Code:
Set oApp = CreateObject("Powerpoint.Application")
Set oPres = oApp.Presentations.Open("D:\Users\JustinBryant\Project_Organigram_24.11.14.pptm")
Set oSlide = oPres.Slides(1).Duplicate
oApp.Run "UpdateLinks2Local"
The code would only work with the 3rd line that duplicates the slide but it all functions well. The link below discusses further on this strange anomaly.
I am open to any suggestions or ideas if anyone has any.
http://help.lockergnome.com/office/c...ict469171.html
Thank you for your responses JohnWilson!