You are using File.execute() to run your scripts, right?
The Toolkit treats the user's Documents/Adobe Scripts folder, however, as a trusted location; when you double-click a JSX file in that folder, the Toolkit does not display the security alert.
So you need to put your scripts into Documents/Adobe Scripts folder to aviod that warning.
But you can use other way to run script: $.evalFile(), maybe should along with BridgeTalk as you are using a "palette" type panel.
Damn, i tried to put them in "Adobe Illustrator CS5/Presets.localized/..." but not in "Documents/Adobe Scripts"...
Thanks a lot