Hi Doug, :)
The problem still exists but I have found a partial solution which I will explain below.
But first I contacted the alarm shop. The guys there agreed to check it out for me but they had a rather unfriendly attitude (they were super-busy installing car audio stuff all day long), and did not give any plausible reason for the malfunction. My gut reaction was that they really were unfamiliar with this installation error and I did not feel comfortable allowing them to trouble shoot the problem, not to mention wasting another day dropping off my car and getting a ride from/to.
So the problem continues, however I managed to find a partial solution. This may seem odd, but it works. When I exit the car I hit the door lock/alarm arm button (on aftermarket remote). Then within a few seconds I disarm the car, then quickly re-arm/lock. Then the system works fine and I can open the doors remotely upon return, without any conflict with the OEM system. I cannot imagine how this works, but it does seem to outsmart the OEM security system.
In summary, now I must hit the remote 3x's vs. just once to lock/arm. It is an inconvenience but I can live with it for now. Because I am so busy with my work it is a major hassle to go to a shop during the week. Maybe in the future I will have a new system installed at a better qualified shop.
I am in the process of installing a DVD system with 3 screens. If anyone wants to hear the story please email me for a report.
Thanks to all of you for your comments on this problem. It's nice to have such a great group of folks to talk about the wonderful Lexus LS.
Mark
Clovis CA