No crank, no start

I have a 2007 Limited 4runner with the 4.0 V6 that is giving me fits.
I recently replaced the 9 year old battery with a new one.
Had no issues with the truck after that for a week.
Noticed then that the rear wiper was not working. Checked all the fuses.
Then found that the rear window was down just an inch or so. Put the window up and wiper was working fine.
Got back in the truck to start it and now it does nothing. I have power to everything. But, turn the key and nothing. No noises, no clicking, nada! Just like that it quit starting. Jumpered from the battery to the starter solenoid and the starter works fine. Jumpered the STA relay in the underhood fuse box and the starter worked. I have meter checked all fuses that apply.
Swapped out the STA relay with a new one as well as both STA fuses and no change.
Tried starting it in neutral and park and shifting it around with no luck so pretty sure it is not the neutral safety switch issue.

Note: The security system indicator lamp on the dash is not flashing. Pretty sure it used to flash. Makes me think the engine immobilizer may have kicked in somehow and shut the engine down. But if I understand that system correctly the engine should still spin over but not start. Instead of the engine just not spinning over at all. Is this correct?

What the hell is going on here? I have been a mechanic for 40 years and never run into anything like this. Have talked to two 30 year Toyota mechanics and am still not getting it fixed. Very frustrated and disappointed in my 4runner. I am a loyal Toyota driver. Never had any issues like this with them.
Can anyone help me? I have gone thru all the threads on this site as well as other sites and so far nothing is helping. It cant be this difficult. I must be missing something simple.

 

I agree with Sean...

 

seans probably right, id start by pulling the battery and letting the ecu reset and seeing where that gets you

 

I did that. A couple times. Once for 30 min. then for overnight. No fix.

 

Well if you rolled up your back window and it stop working, maybe the alarm system is hooked to the back window??? Try rolling it down a bit and see if it starts? Always go back to what you were doing when the problem occurred.

 

Good thought, put the window back down.
No start.
I have since tried jumping the starter at the solenoid direct from the battery and had someone turn the key at the same time. The engine turned over but No start.

 

i figured you did but thought i might as well say. do these motors have an immobilizer?

 

If I get time tonight I will comb through the schematic and see what could prevent it from starting. MY main guess is the alarm system, the question is the alarm factory? If the light was flashing and everything is working and now the light is not flashing and it will not start with the key, seem to me the alarm has disabled starting. I will look and see if they have factory alarm wiring in the factory manuals.

 

Discovered the ETCS fuse, #24, was blown. New fuse, started right up.
Thanks for all input.