I had a similiar issue when the Add-In was searching for a file that could not been found at the location specified.
In my case i used a XML file to store user settings. I hope this info might help you.
When I ran the script after registering the Add-In, everything worked like it should. I'm wondering if there was some sort of time-out for the post build events, and if one of the events took too long it would go ahead and complete the build and start SolidWorks with the product unregistered. The files that my script copied in are dependencies of dependencies. Without which the software won't run properly.