My apologies. There’s an expert preference that sets the default value for code signing on export only, and I’d forgotten I’d changed it to true.
So I can now reproduce the problem.
Thanks for all the feedback — the issue will be addressed in a forthcoming maintenance release. In the meantime, please use the workaround of a second save.
FYI, the Script Debugger.plist file turned out to be a red herring.
Was this issue fixed? I am able to codesign without issue when manually saving out an application but I am encountering an error while trying to AppleScript Script Debugger to save out codesigned, run-only apps. The Save and Close (with saving options) functions are automatically reverting all saves to Do Not Codesign.
Attaching a screen video to show it in action (sorry that the volume is low).