AutoIT Script waits for Logon

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We recently created an AutoIT script to install Faxgate. The problem we're having is that once we advertise it, it won't process anything more in the script other than the "run setup.exe" part of it (i.e., it won't process the winwaits etc..). Does anyone have an explanation of this for me? What i'm really wondering is if AutoIT is going to work, because it waits for a window to pop up to continue.

?? G-man