When I got my 1999 LS400 the only key was broken to the point the blade was about to part company from the casing so I had a new one supplied,cut and the guts swapped over.
Putting it in the ignition I noticed the security light remained flashing and of course although the engine turned over it wouldn't start.
Thankfully this had happened before and some kind member of the LOC had posted up the solution, insert the key turn to ACC and leave for 6 minutes.
I did this but the light still continued to flash, I removed the key despairing of ever having the car run again, a little later I reinserted the key and lo and behold the light went out and the car started.
So the missed line was to remove and reinsert the key after 6 minutes.