R/S on 98 Jeep Grand Cherokee

Hey all:

First Post is a question...I know, bad form ediquite...

I put a remote start system on my 98 limited.  I set it up to work with the factory keyfobs (three lock pulses) and it starts fine.  However, while the car is running, the rest of the keyfob is inoperable, just like if the key was in the ignition.  Does anyone know how I can disable this feature so I can use the factory keyless to start the car and then unlock the doors while it is running?  Wire colors are helpful as my schematic is crap.  No transponder or anything on this model to worry about.

Thanks

Brennan