I am having the exact same problem. We upgraded to R80.10 on the mgmt server with R77 gateways. Everything was working just fine. Then we upgrade the gateways to R80.10 and all the sudden our Application clean-up rule was blocking tons of web traffic that was not hitting the rules above it, even though with the R77 gateways it was working correctly.
I turned to the logs to find out what was going on and to my shock, the Application logging is drastically changed! When I filter for the Application Control blade, I see traffic for it, the correct icon appears in the Blade column, I see application names BUT... the "Access Rule Number" and "Access Rule Name" are showing the firewall rules information, not the application rules policy. So all the sudden, I no longer have visibility as to what in the world is going on! I have noticed that if the Action is either "DROP" or "REDIRECT" that it all the sudden shows the Application rule number and name, not the firewall rule number and name. However, if the action is just Accept (which 90% of the traffic is) it no longer shows the App rule/name but the Firewall rule/name. This is so frustrating.
Per the recommendations on this thread, I made sure I'm running the latest Jumbo hotfix across my entire environment and I also changed all App logging to be "Extended Logging" but neither of these made any difference. That data is clearly there (even prior to those two actions) because if I double click on a single entry, I can go to the "Matched Rules" tab and see both the firewall rule AND the App rule listed. So clearly, this is an issue with the SmartLog viewer deciding to show the firewall rule/name in the view when the action is accept, but ONLY for R80.10 gateways. I still have some R77 gateways and their logs still appear just fine in the SmartLog viewer.
HELP! This is driving me nuts! I lost my ability to easily filter and see what was going on with the Application Control blade! Is this a bug or are things working (horribly) as designed?