Factory installed alarm system hindering start?

[AirForceMom]

My 2000 Mustang (v6) has an alarm system that disables it from starting unless the little pin is inserted (just under the dashboard) prior to inserting the key. It is a manual transmission which means the clutch also must be fully engaged. My problem is this. I insert the alarm shut off pin, then put the key in the ignition and turn but sometimes nothing happens. It doesn't turn over or anything but all gauges register. It acts like I have not inserted the alarm pin. After pressing and releasing the clutch many times and inserting and removing the pin just as many times, it will finally start (so far anyway). I have begun leaving the alarm pin in all the time but even with the pin remaining inserted, today it wouldn't start (until I finally got angry and swore at it.. ha). Could this be the sensor for the clutch malfunctioning and not the alarm system? If that is the most logical issue, is that a difficult fix? If it's the alarm and I were to remove the alarm system, could that fix the problem? The car is just now out of warranty.... figures... and I dread the thought of a repair bill. Any ideas or advice would be greatly appreciated!!!

Thank you!!!