Custom applications published from pre Orlando will not be visible on "My Company Applications"Module on Orlando ; but will be visible on "All Applications" module.
There is a possibility that this will be an issue only on PROD instance.
This is driven by a flag called "Shared Internally" on the sys_app_store record of the application.
This will be false on the instance where the application will be missing on "My Company Applications" module.
Please install/update the application from the "All Applications" module and this will fix the "Shared Internally" flag on that instance
After this, the application will be visible on "My Company Applications" module as the flag is set to true with the above update.