Scripting

I am trying to create a silent install for a product that uses an msi, but kicks off another configuration utility at the end of the installation. This utility messes up my silent install so I have scripted the install with AutoIT so that I can cancel out of the configuration utility. That works in testing, however, it doesn't work when installed on workstations where no-one is logged on. The AutoIT sendkeys function doesn't seem to work when no-one is logged on. I have worked around this type of problem in the past by repackaging, but I really don't like to do it. Does anyone have any ideas? -Thanks