I figured it out! But now the question is why...
I have a set of high-end walkie-talkies plugged into the in the center console, the moment I unplug them the locks work as expected just fine. When I plug them back in, I have that issue! The 12v outlet isn't supplied power when the car is...
So just got back from the dealer, they had a technician troubleshoot it for a couple hours and were unable to find the cause. They need to bring my truck in for a few days where a technician will be assigned to it, they believe they will need to get on the phone with the engineers to discuss...
Ugh, I just got my 4runner last weekend and I'm already noticing issues! I've loved 4runners forever now and finally got one, let us know what you find out!