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I would suspect it needs the power cell in the key fob replaced.
It may have enough electricity left to work the little LED indicator but not enough to transmit. If this is the fob you use most of the time it would make since that the battery would be depleted before the other just because of the higher use.
Replacing the battery cell in the fob is what I would try first.
Double check the area where your remote is not working. These new key fobs manufacturers are using still operate on RFID signals if I'm not mistaken and those signals can be interfered with by technology transmitting these same signals within 50-200 ft. It might not be your "new electronics" might be your neighbors, or the power company has their low frequency signals interfering with your signals. Do a public search on your neighborhood and find out if any new electrical work has been done to your block.
Remote Entry Receiver is inside the back lift-door panel. Open the panel and check the receiver antenna (a wire hanging out from the receiver). Try to stretch out the antenna as far from the receiver as you can so the receiver gets the maximum range for signal receiving. Since you said you had the FOB tested and it worked fine, your signal transmission side is OK. The issue is at your receiver side. Good luck.
You could possibly have a blown fuse, or a bad switch. The shifter interlock is controlled by the computer and it looks inputs from the key transmitting the right code, the ignition switch in the run position, and the brake pedal being pressed. If any one of these signals is missing the computer will not unlock the shifter. Another possible problem could be the interlock mechanism itself, malfunctioning or being damaged in some way. I would reccommend taking it to your local dealer and having it checked out, but only after checking all of your fuses, and the owners manual for other possible problems. One other thing, would be to check the battery in the remote on your key. If it is dead, it may not transmit the code to the computer.
my first thought was batteries in the remotes. how do you know they are still transmitting? or if they are, if they have sufficient power to broadcast the signal that it can be picked up by the receiver? if you can access the bcm, i'd look for that data. once that is determined, then it's a matter of tracing backwards until the problem is found. personally, i prefer to start at the end (in this case the actuators in the doors) and work backwards. the most common problem in any electrical malfunction is loss of ground. power second, and failed hard parts third.
Regarding the remote transmitter issue: Take the remote transmitter to your Toyota dealer. Ask them to test your transmitter with their hand-held RF detector. All Toyota dealers are required to have one of these devices. The RF detector will test the remote to see if it is indeed transmitting the proper RF out of the transmitter, and the strength of the RF signal. If there is no signal, the remote has failed (unfortunatly common), and the remote will need to be replaced and reprogrammed to the vehicle. I do this quite regularly, and rarely do I tell customers taht they need to spend 800 dollars for such a simple diagnosis/fix. The keyless system is very reliable. I rarely change the ECU for the keyless, unless somebody somehow gets the ECU wet, then it def needs replaced. Hope this helps.