You need to open the presentation itself without a window.
Something like the following would work:
Dim oPPTApp as Powerpoint.Application
Dim oPPTPres as PowerPoint.Presentation
Dim sFileName as String
Set oPPTApp = New PowerPoint.Application
sFileName = "c:\some_folder\presentation.ppt"
Set oPPTPres = oPPTApp.Presentations.Open(sFileName, WithWindow:=msoFalse)
' Do your stuff
Don't use the .Select method or do anything that references the document window, activewindow etc.