Car Alarms: electric windows, lincoln ls, electric windows

Question
my electric windows will not work due to alarm.  would can be done?

Answer
The only ways I can think of that the alarm would interface with the windows is:

1.  There were window rollup/down modules installed and integrated with the alarm.  

2.  It is a European vehicle or something like the Lincoln LS that allows the windows to roll up and down if you hold the key in the door to either open or close and the alarm is locked up providing a constant output to either lock or unlock.

These are the only situations I can think of that would cause the alarm to interfere with the windows.  Other than a fuse blowing.