Maybe they programmed the hood switch wrong, if they even installed it. I know when I went to get my viper 5901 installed, the install shop didn't hook up the hood pin. Hell, with my parent's cars they didn't get the hood pin installed at all. I bitched about that and said its nice for the alarm feature and really great for if someone hit remote start while you are tinkering under the hood. They put it in for free but brought up the idea of a mercury switch instead so its a sealed unit that can't rust away. The hood pins that your alarm came with work but they corrode over time and can make false readings.
First thing to try is to see if you can find the hood pin when you pop the hood. Some places put it on the fender edge, others will put it on the front support rail, some put it on the lip that is right below your wiper cowl. Try to check those areas for the pin. Once you spot it, try to remote start your truck with the hood up, if it starts, that means they didn't program the switch polarity right on the module for your remote start and its a quick and easy fix. If it doesn't start then try to either push the switch down as far as you can or disconnect the little wire that is pushed on the pin. If after doing that you can start it, your pin is either not getting pushed down far enough with the hood down to disengage the safety feature or your pin is not making good contact and needs to be cleaned up.