Follow the references in it, and compare it to your file.
I'd start with what happens when the activation link is clicked.
At some point, it updates the information in the DB, so it knows what plugins to include with the site. You may wish to consider making it a separate db value, so that when someone cancels and goes back to a regular account, they don't still have it listed in their main plugins value.
Come to think of it, that may be your issue. Off the top of my head, it's going to try and load the plugin referenced in the db out of the plugins dir. If it doesn't exist, it takes it out of the db. So if you just flat out delete a plugin, like it was causing issues or something, then it's removed from the array in the db.
So, in theory at least, if it tries to load the plugins from the db array, but it doesn't exist in the plugins dir (although it is the premium dir), it won't ever actually be activated.