Plugin wont work correctly with Prosites

Have an invoicing plugin that I want to make available on a specific level (2 of 3 and above). Using the premium plugins module to manage this. When testing a site to see if the plugins are all working, this particular plugin appears as it should on level 2 but it will not actually work (create invoices/add users etc.) right off the bat. I've figured out that I can make it work by manually upgrading the site in pro sites to the top level. This fixes the problem and then I can downgrade the site back to the original level and it will continue to work fine. Would like it to work properly from the start however.