the horn honk on lock is a default setting. you will have to go and turn that off. I would still have the alarm shop check it out and make sure. I don't think the flash would have messed with it since its an aftermarket alarm and controlled by its own brain and not connected to the ECM of the truck for any monitoring other than the remote start function and door locks.

 

I know this sounds like a pain but . ... when you take your truck to the dealer show them what works with respect to these 'special' features. Afterwards if they don't work then guess who has to make it right - and right now!