For those who have a similar problem, this is how I solved it.
It seems that opening the drivers or passenger doors with the key can cause the alarm to go off. I now always open the trunk first which opens all the locks.
If the alarm ever goes off, this is how I reset it.

1) Remove the alarm fuse. (number 15)
2) manually lock and shut all the doors
3) lock the trunk with the key
4) have someone hold the hood switch closed or tape it down so that the alarm system thinks the hood is closed.
5) connect the fuse
6) open the trunk which should unlock the doors
7) release hood open switch

At this point I can lock the car with the door key and all doors lock. I only open the car by opening the trunk first and I have never had a problem with the alarm going off.