Issues with Active Setup
Check the contents of the package and make sure that you've not got anything undesirable in there that isn't directly related to the application.
ActiveSetup itself isn't going to be the issue, but whatever you're running/repairing may be.
I agree with the above.
It sounds like you have installed an app on your users machines, and since they now have a problem, obviously it was caused by your MSI with the ActiveSetup stuff.
Do any of your MSI's have active setup?? or has someone just read something about ActiveSetup??
How many users is this effecting?? What OS are you running on??