For about a year, I was having a similar problem with the tailgate as JrAdrock80 described. After disconnecting the battery to replace the stereo I lost wiper/defrost/latch/lock controls. At that time the window would still go up and down, but I needed to reset the top point every time I wanted to open the tailgate. Nothing would function without the ignition in the ON position and the top-point reset.
A few months ago, the window stopped functioning. The backup camera that I installed requires power from the rear tailgate and it works just fine... just nothing else on the tailgate.
-I tried the 2 key thing that Oneluv13TR4 described... with no luck
-I put a 12V power supply to the rear window motor... and it functions as it should
-I tried getting the wiper back to proper neutral position... with no result

Any new ideas would be greatly appreciated

Finally figured it out......... It wasn't in lock down, it was a bad wire in the hatch harness. The blue/red power wire was broken in the hatch rail on the side of the hatch. I found a thread by pure luck and someone else had the same problem as me. I soldered in a small length of wire to fix the broken wire and now my hatch is FULLY functional again.

If it wasn't for that random find I would have pulled my hair out trying to figure this problem out. I still cant believe it is fixed at this point.

Same question. It seems like no defroster is "better' becuase it's just the initialization. Anyone have any luck getting the wiper/motor running who did have rear defrost?

Sounds like the issue that I finally figured out. Its a wiring issue in the hatch.

Get a multimeter and take the panel off of the rear hatch. On the body ECM there is a blue connector. Disconnect the blue connector and probe the solid blue wire. This should be 12 volts with the ignition off. Next probe the blue/red wire and this wire should also be 12 volts with the ignition off

If both are 0 volts, then it's the wiring in the hatch. You can pull the boot off between the hatch and the body of the 4runner at the top left of the hatch opening. When you expose the wires, you should see the solid blue and the blue/red wire. You can use a sharp probe or a needle to pierce the wires and check the voltage. If both are 12 volts at the top of the hatch, you have a bad wire or wires inside the hatch. You will need to find where the wire is bad and splice in some new wire. Or you can splice at the top of the hatch and run a new wire down to the connector.

Good luck. I can try and take some pics if you need them.

Would love to see some pictures.

I noticed my PO applied some sort of sealant over the boot(presumably it was cracking?). Is there a way to remove and replace this boot without hating myself?

thanks for this thread. Solved my rear wiper problem

Thanks for the ideas JrAdRock.

I probed both wires at the blue connector with the ignition off. The Blue wire had 12 volts, but the blue/red wire had less than 1 volt (but not zero). I probed the blue/red wire in the top left of the hatch - as you suggested - and found that it had 12 volts at that location. I cut the blue/red wire in both locations and ran a new wire between which gave me 12 volts at the blue connector again as is necessary.
I thought my problems were solved after finding this smoking gun, but not a lot has changed with the lack of power back there. Shortly after, the door ajar indicator started functioning on the tailgate because the dome lights stay on and the tailgate key hole can now lock/unlock all the doors, but I still have no window/washerpump/wiper/latch controls back there. I connected a power supply to the wiper motor and it oscillates from return poistion to furthest poistion smoothly and consistently. So, the problem is not the wiper motor.

Any other thoughts would be greatly appreciated.

Well, It's fixed.

In case any of you go through the same nightmare I did, don't go to the stealership. It turns out that the Tailgate Lock Actuator Assembly was malfunctioning and needed to be replaced. I also must have fried the Window Motor when I plugged in the power supply.

I replaced the Lock ($200), Window Motor ($300), and Window Regulator ($200) for which the dealership wanted $1700 to do. Everything came back up as it should operate.

Note: If your tailgate needs the window point set every time you want to open it, a simple check of the fuse labeled "ECU-B" under the hood could also be the problem. I knew I shorted it out during the install and I replaced it right away. Remember to disconnect your battery when working with electricity.

This forum is a big help! Thanks, guys. Happy to have a fully-functional vehicle again.

I'm new to the forum and I recently bought a 2007 4runner sport with 4.0 motor. I have the exact same issues everyone else is solving with the rear window up/down fix, but mine won't reset. I have searched the forum and to find answers and checked fuses, child safety locks, did the lock down fix reset, rolled the rear window up and down from dash switch and rear key to no avail. I even unhooked the battery to reset everything and the drivers window express up/down work, the sunroof opens fully with the one-touch feature but still no dice on the rear window auto up/down, no key fob acuation of rear window, no rear wiper/washer function, no rear defrost light on dasy.
When I bought it, the rear hatch wouldn't open and the previous owner accidentally broke the rear wiper using the window down feature to move things in and out of the rear compartment. I did not attempt to use the rear wiper or washer prior to buying because of it being broken. After some blood/sweat/tears I removed the rear hatch panel, popped the back with the two lever switch and sprayed WD 40 on the mechanism after removing the 3 bolts holding it in the hatch and it functions/locks completely. Replaced the rear wiper arm (extremely painful to fix due to rust and the splined shaft) and wiper with genuine Toyota parts, have wiggled the wiper to make sure it is in the neutral position and still not working.
Sorry for the long post but it helps folks to know the history and what I have done so far because I'm concerned I could have unknowingly damaged something while in the tailgate or previous owner damaged something when he broke the wiper arm.
Also wondering where the safety sensor is in the rear door that determines fully up because a bad sensor would not allow a reset, thinking the rear window is not fully up. Thanks

Thanks so much for posting this! Solved my rear wiper problems!

I had the same exact symptoms you described on my 04 limited I just bought, and your solution worked!!! Thank you for your post, I would of never thought of trying that. Also note I examined the rear wiper and rear window position prior and everything look closed and in place properly. I went in the cabin, pressed the up arrow and I thought I heard it move a smidge, then my rear defogger and wiper worked. thanks again.

Hi Brian, have you ever figured out what that was? I have a very similar issue:
* Rear wiper does not work
* Rear window does not work (if I disconnect & re-connect the battery it starts working until I try using the rear wiper, then it stops working)
* Rear defroster works
* Rear washer fluid works

Rear window has been homed and all the way up.

Just try switch down the rear hatch window all the way down and then switch it up till the window stops then release the switch.

Keep trying 2 or 3 times. It should work.

Good Luck.

Try resetting ECU by disconnecting and re-connecting the battery, then try the back window down/up.

I had a problem with my rear window to. It would not go down and the wiper would not work. I though it was hopeless unit one day after washing my car it just started working. What had happened was I had rolled down the window to haul some pipe and the wiper resting position had been changed. If the wiper is not in the correct resting position the window will not role down and the wiper will not work. I suggest playing with the wiper position until it starts working again.