I wouldn't rip the system out just yet.
If its working just be patient alittle longer until we find out exactly what is going on.
The remote that you have looks like some of their R/* remotes too.
I doubt that your vehicle has 2 different systems (seperate brains for R/* & Alarm)installed as this is usually a pain to get them to work properly. Most units come with one brain that functions as a "combo".
Is there a alarm siren under the hood ? When the alarm starts sounding is it the horn or a siren ?
Alot of times Installers will hook up the horn to the R/* apon request so that it seems more like OEM. For example with a factory FOB you press the Lock button twice and the horn honks as confirmation.
The R/* is connected to the car to disable the factory alarm or the factory anti theft before remote starting. You do not need manuals for both.
I wouldn't rip it out yet.........we will get this working for you
Contact Commando directly and give them the FCC numbers on the back and let them take the guess work out of this for you. They will be able to tell you for sure what unit it is and provide you with a manual and remote.