Okay it goes something like this !!
My master key was stood on and broken [ by the previous owner ] , push the lock button and the red light flashes but it does not flash for unlock or trunk but it will lock the car but not open the trunk or unlock the car .
To start the car I have to insert the key into the ignition lock , there is no proximity operation .
The previous owner had a lock/unlock device installed on the car , so I have an aftermarket fob with two buttons which will lock unlock the car and then I use the Lexus fob to start the car after I insert it into the ignition lock .
I have seen the device inside the drivers door spliced into the loom .
I have just acquired a spare master key and have managed to reprogram it to start the car BUT ONLY when I insert it into the ignition look , I have no proximity function at all .
Is this because my original master key has no proximity cos its broken ?
Or should that not matter ?
Also I cannot seem to program it to lock/unlock the car .
Initially I thought that I would have to remove the aftermarket door lock device BUT the broken original master fob will lock the door even with the aftermarket device still hooked up ??
HELP !!

 

Have you checked the button under the dash?
Right next to the tire pressure reset button there is a proximity key button. Mine was off when I bought the car and just assumed over 15 years something had gone wrong with the system but whatever no big deal.
Found a post on an here about the button, pressed it, and it changed my life

https://www.clublexus.com/forums/ls-3rd-gen-2001-2006/456915-smart-key-no-longer-works.html

 

Turns out under dash proximity switch was off !!
I had no idea it had one .
Original broken master key now works proximity wise but not the extra recently programmed one , the extra one will still start the car inserted .
I will redo the programming and see if that makes a difference .

 

Can you not just buy a new plastic shell and transfer the guts of the broken key to it?
Then keep your new one with no proximity as a spare?

 

I wish , red light only flashes for lock function , no red light on fob when pushing unlock or trunk button .
Have had it apart and the board is smashed and I have been hesitant to mess with it as that's the only one I have .
Now that I have a spare I will see if I can repair it .
I figure the proximity function might not program in if the under dash prox switch is off ??
Will try reprogramming later and will post the result .