Endpoint Central and Application Control Plus, though seamlessly integrated, aim at giving different perspectives of the application data to its users.
As the name suggests, the Inventory module works on giving a granular view of the networks software repository, displaying even different versions of the same applications as separate entities. Whereas, Application Control's application discovery tool is meant to give its users application data in the most succinct and concise form, enabling them to arrive at easy but informed decisions regarding security policy creation. Instead of showing different versions separately, Application Control simply displays it as a single product.
The objectives of the data represented also vary. The Inventory module is meant to provide SysAdmins with management related data, while the Application Control module presents data that acts as a foundation for security policies. This is why Application Control also tracks all running processes and executables, satisfying the users need to achieve both application and process level control. While Inventory on the other hand, is an organized collection of the installed software with attention to granular details.
These differences in data representation is why there can be a mismatch in the count displayed.