problem with astrostart remote starter

I have recently installed an astrostart remote car starter in my car.  Its a manual and everything was working fine, however, I just had to replace the battery in which the car sat for a few days until I could get a new battery.  Now the remote on the starter does not seem to be working.  I apply the emergency brake twice and the car does just what it should, I exit the car, and it shuts down just fine.  However, when I go to hit the button to restart it does not work, the brain does not even respond like it is recieving a signal.  I went through the process of putting the #8 dip switch up so it could relearn the transmitter and still nothing.  I have gone through everything to make sure nothing came loose or disconnected.  I am at a loss as to why the brain does not respond at all to the transmitter, has anyone had a similar problem, or know another fix to the situation?

process of elimination.
The battery in the remote - check and replace as needed.
test all connections with a computer safe test light.
Check for hood connection false hood open, check brake input to make sure it isn't seeing 12v by mistake.
If all connections are good then try unhooking the brain at the main harness for about 5 min then reconnect. Relearn remote and see if it responds.