I have created a script that pops up a custom dialog box warning the user that they are about to be logged out due to being idle beyond allotted time. I have set up a Install OnTimer script that initiates the custom dialog box warning and if the user hits OK then it resets the Install OnTimer Script and they have bought more time. The problem I'm having is that if the user doesn't hit the OK button and is idle too long the script is paused indefinitely and I can't close the dialog box and thus log-out the user. How might I get around this?

Don't use Show Custom Dialog[].

Use a dedicated layout conveying the message and having the appropriate "dialog" buttons.

Pause the script for the time you desire to use as a timeout for the dialog.

If you are particularly crafty, you can put a Web Viewer on the layout with some JavaScript displaying a countdown. This is more elegant than refreshing a layout in a script loop.