There is not enough data there to go on from what you say above, but here are some things that come to mind. First of all, Windows (and not the installer!!!!) displays the "not responding" title bar message. So I assume you are launching another program with a "wait" option enabled.

1. Make sure you are using the very latest SB72 build.
2. Make sure you do not have a bug in your script coding.
3. If 1. and 2. does not help, display a "Wait Dialog" with the "Start on separate thread" option enabled.

Hope this helps.

Lindersoft Emergency Support