You didn't mention your OS.
In Windows case, User Account Control (UAC) is a real expert in being really annoying.
Might it be a culprit? I'm always keeping UAC completely off and never encounter such a popup.
And admin rights for ID user should go without saying...
If this is not the case, and assuming your script is jsx, maybe adding these two lines to disable/enable warnings might help:
app.scriptPreferences.userInteractionLevel = UserInteractionLevels.NEVER_INTERACT;
app.scriptPreferences.userInteractionLevel = UserInteractionLevels.INTERACT_WITH_ALL;
FWIW: This question seems to be related to this thread in the Adobe InDesign Scripting Forum:
it would be better to post script related questions in this subforum:
Moving to InDesign Scripting forum.
Yes sorry- I'm running on Windows 7. I made sure to completely disable my UAC, but I still receive the popup. I'm inclined to believe InDesign is providing the popup, not Windows maybe?