Apologize in advance if this has been posted before, but was unable to find through searching.
I'll give a quick rundown of the history of the vehicle's service:
1999 LX 470, bought 4 years ago, has ~$180k on it. About 3 years ago, put the key in and when turning to start something popped and key moved freely in the cylinder. Had the ignition cylinder (?) replaced at Lexus dealer and everything fixed.
Fastforward to a few months ago, went to a movie and car was dead, i believe from alarm running for a couple of hours, also had old battery. Replaced battery, father-in-law hooked battery up backwards, but after changing about half the fuses, we were back in working order. Around the same time, we also had trouble starting in a parking lot. Car would crank but wouldn't start, appeared to be a fuel pump issue, but upon inspection/repair by mechanic, mainly just replaced fuel filter and a couple of minor things.
Now, a few weeks ago, began having intermittent starting problems - similar to the last, where the car will crank, but will not start up. The problem was tracked down to corroded fuse box and bad ECD relay, so had fuse box cleaned and replaced relay, short in wire from relay to engine was traced down and repaired. The result was that the car would now start up, but one thing they noticed was that the key had to be held together just right (key was broken, the kind with a single screw holding the whole thing together) to get the car to recognize the key, because that was also causing a problem with the fuel shutoff from security system.
So, had key replaced at Lexus dealership a couple of days ago, and here we are today with car not starting 90% of the time because when key is put into ignition, the red blinking security light continues to blink, and when turned to on, check engine light does NOT come on, which i understand is suggesting that the problem is the anti theft system not recognizing the key. There have been a couple of times when it did recognize it and started up. So, I'm wondering where to proceed from here. Is it possible that the transponder in the key is bad? As i've had some shorts, and blown fuses in this vehicle before, could it be wiring that may be shorting the system out? Any way to by-pass the security system?
Sorry for the length. Appreciate any help on how to proceed. I intend to call my mechanic to see what he suggests, but my guess is that he doesn't want to see this car ever again.

Thanks,
RJ

 

Have you tried replacing the battery in the key? And when you say you had the key replaced at the dealer, im assuming it was just the mechanical part of the key, not the immobilizer part with the buttons? I would probably start with a new battery, then move onto a new key itself. I would also check to see if there are any codes stored in the immobilizer system.