Had the same issue when installing the Presenter patch. Could you go to the Powerpoint Options (under the Office button upper left), to Plug-ins and then look if the Presenter plugin has been deactivated (not sure of the right terminology, because I'm using a Dutch version of PPT)? If yes, you should be able to reactivate it from this menu. I will try to find the thread in this forum with a more detailed explanation if you do not succeed.
PS: here is the thread: http://forums.adobe.com/thread/506350?tstart=30
Sounds like the Presenter addin has been disabled by Office.
In the application, click the Microsoft Office Button.
Click the <ApplicationName> Options button.
In the categories pane, click Add-ins.
In the details pane, locate the add-in in the Disabled Application Add-ins list.
The Name column specifies the name of the assembly, and the Location column specifies the full path of the application manifest.
In the Manage box, click Disabled Add-ins, and then click Go.
Select the add-in and click Enable.