autopage rs 727 remote start issue

This was my first install. I only bought the Autopage RS-727 for its remote start and keyless entry, not for the alarm. Its installed on a 1990 Toyota Celica GT. I tested everything  prior to finally connection and after it all was soldered. Everything worked on it. Its only been in the car for a week. No here is my issue. It seems that when I remote start my car, and before the car warms up, I can disarm the alarm and get in. But if I remote start the car and the car is either already warmed up or warmed up from the remote start, the alarm will not disarm, nor will the remote start kill from the FOB. It seems as if the alarm brain will not respond to any commands from the FOB. So in order to get the alarm to disarm, I have to open the door with the key (alarm sounds), kick the brake pedal to get the remote start to de-activate and then the alarm responds to FOB with me pressing the un-lock/disarm button.  Can anyone please help me.

Maybe try relocating the antenna to the bottom of the windshield. Also check and make sure you are getting your ground at the kick panel (paint free). The last thing that I would try is relearning the remote to the system. Hope this helps.Where ever there is a problem there is opportunity.