What is your clean-up rule in Application ordered layer? That should be set to Accept and I recommend a Detailed logging with it's default configuration of Accounting and per Connection enabled:
This should log all traffic and applications if there are no other issues.
Obviously, the gateway handling this ordered policy needs to also have Application Control and URLF blades enabled.
Once you've established that you are logging what you need, unchecking the "per Connection" field will reduce the logs by not explicitly logging the Firewall established connections.
Also ensure that you don't have the Application ordered layer defaulting to an implicit Clean-up rule with drop, which is the default for new layers.