What was the issue with the windows? It doesn't sound like it was the alarm system brain.
I have a module that interacts with the alarm brain to put the windows up when I hit the remote lock button. The wire to activate the module needs to give a ground signal. Turned out to be a problem with the valet switch for the alarm which killed all the outgoing signals. The window problem was just a bad connection at the connector for the harness . I was looking for new terminals for the connector at the window switch but no luck finding them so that means I have to replace that harness even though the one in my car is perfect except for the terminals....sh*t like that bothers me.