Normallly when you open two PowerPoint documents they open in the same instance of PowerPoint. This makes it difficult to compare two presentations. The solution is simply to open another instance of PowerPoint by using a second user account.
In the Start menu, SHIFT-right click the PowerPoint icon, choose "Run As" and enter the details for the other user. You need to have Admin privileges to do this.
You will also find that the second instance saves by default to the second user’s "My Documents" but this can be changed in Tools > Options > Save tab.
I was then able to open separate PowerPoint presentations on each monitor!