Make sure your hood switch is adjusted correctly. The hood is likely to deform slightly under high heat causing the distance between the switch and the underneath of the hood to get bigger. So what could be happening is the switch going to its released position and triggering the alarm. Try to adjust it a little higher so it makes better contact with the hood when closed.
I had a similar problem with the alarm randomly going off. I bought my car with a carbon fiber hood on it which flexes very easily. Every time it was windy outside the wind would find its way under the hood and lift it a bit causing the alarm to go off. I just disconnected the hood switch and never had a problem again.
