I'm seeing the same issue on a new upgrade to 3.1.3 from 2.4.6 - it prompts about incoming network connections on every start, no matter whether I accept or deny, and no matter that it's already allowed in the firewall settings. Has anyone found a way to make it stick?
Update: Looks like this is because the app isn't signed, so the firewall setting won't stick by design in macOS Sonoma 14.7.