I have the Snow Leopard firewall enabled, and every time I run an application for the first time the OS asks me whether I would like to authorize that application to receive network traffic. [See attached.]
The firewall, however, is unable to retain the authorization for DevonThink Pro Office. I am prompted each and every time I open the application, even if I close and run it again in the same user session (i.e. without logging out in-between).
I have not encountered this problem with any other applications.
I encountered the same thing with Leopard once and fixed it by doing the following:
Quit DT
Set the firewall to accept all incoming connections in System Preferences
Delete the firewall configuration preference file ‘your_hard_drive/Preferences/com.apple.alf.plist’
(note: this is in the drive preference folder, not the user’s preference folder)
Set the firewall to set access for specific services and applications
Manually add DT to allow incoming connections and quit System Preferences
Launch DT
You may or may not get the notice to accept incoming connections at this time, but if so, once you accept you should not be asked again. Note that this worked on Leopard, but I don’t know if Snow Leopard is any different.