98 Grand am passlock 1

My sisters remote start was working great for about a month then it just quit.  I replaced the brain of the unit and had it working for a while.  The next morning the car started with the remote start but after that it would only crank.  I thought since the R/S brain quit working that maybe the passlock module needed to be replaced too.  So I did with the new 556lw,  the new 556lw does not want to learn the codes.  Is there maybe something wrong with the passlock system on the car why it will not start with the remote, but works perfectly fine if you use the key.  Any ideas would help.

Thanks