A few days ago i found out the same think. Terminal returns "a sealed resource is missing or invalid". I thought it has something to do with the update but i'm not shure.
But i didn't get questions/warnings from the application firewall for Safari. Maybe because i didn't add Safari to the app-firewall because for me there is no reason to do so.
But since i installed 10.5 in autumn 2007 i get this question from the app-firewall for incoming connections when i open Word, Excel or sometimes even Skype. It only happens after a restart and just once. But it is annoying!
I then decided to check if the problem is related to the digital signature. So i restart the Mac, checked Word and Excel in Terminal with the codesign command to see if they are signed. They are! I opend these apps wich is followed from the anticipated question from the app-firewall. At this moment i send the command in Terminal again to see if something is wrong with the signature but they were ok!
So what ever is the problem with the application firewall and some apps it seems to have nothing to do with the signature.
For me there are two questions. Why Safari 4.0.2 is'nt signed correctly? And what i can do for stopping the app-firewall from ignoring the settings and asking every time again and again and ...