"you are opening application "xyz" for the first time are you sure you want

When working in Tiger or Panther if I click on a document eg: word, illustrator, photoshop, indesign. and the application that is supposed to open this document is not open already. You get a warning message. that says "you are opening application "xyz" for the first time are you sure you want to open it. " Even though this is not the first time the application has been launched. However if you launch the application from the applications folder or from the dock the warning does not appear.
How do you disable this warning or at least correctly inform the OS that the application has been opened before.application
This happens from clean installs and those that have their launch services database cleared the link from document to application survives a logout but not a restart. I know it is a security feature and not a bug but it would be nice to know where this cache/.plist is and why it is suffering from amnesia.
Textedit does not exhibit this behavior across installs but any other app does I get the warning whether it is a user with a l

Michael,
This could be related to the Side effects of System cache cleaning.
;~)

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