I've looked literally everywhere with every dang search term I can think of, and I guess either no one has this issue, or nobody ever tries to do what I'm doing.

First off, I have a first gen. 1991 LS400.

What's happening is:
Let's say I walk up to my LS400 and open the door. With the keys in hand, ignition off, in park, everything off including headlights, etc, and with the door open, if I press the lock button to lock the doors from both the driver's side switch and the passenger side switch, all doors will lock like normal, but then immediately unlock!! No matter what I do this will happen.

If I close all the doors and do the above from inside, every door will lock and stay locked. Also if the doors are closed, I can lock the car from the outside and it stays locked as well. So this is only related to having a door open!

Also the factory alarm/immobolizer was disabled/bypassed by the Lexus dealership, but not sure if it's related? I sadly don't remember if this happened before/after that modification.

But like I said, every single thing operates normally except for locking from the button with a door open 😒

On another note, I am attempting to repair the plastic peice behind the key cylinder and I noticed that the wires don't do anything different when touching them. For instance, if I touch the power wire to one color, the door locks. But if I touch it to the other color, it locks as well. No unlock function at all from the plastic peice or the wiring! Probably gonna start another thread on that, but wasn't sure if it might be related to this automatic unlocking?

 

this is a normal feature of the car!
the locks will not stay locked using the lock/unlock button to prevent you from locking the keys inside as the door stays open.
back in the old days you would have to hold the inside door latch handle open in order to lock the door.
this "feature" is doing the same thing, to prevent you from locking the door from the inside.

thus, this is not a feature of the immobilizer.

 

My 89 Celsior (same as LS400 90-92) does almost the same thing.
And yes, I just went and did battle with my car for more time than I would like to admit to make sure I got this right.
Initially I had written up a whole stack of conditions when things happen, but it all boils down to this (at least with my car).
* If the key is in the ignition (just has to be in the ignition, does not need to be turned) and either one of the front doors are open, it does the lock/unlock dance when I try to lock from inside the front door via the armrest switch (either front door).
* If the keys are NOT in the ignition, the locks behave themselves completely regardless of doors open or closed.
* The locks next to the inside door handles stay in place when toggled. They dont operate any other doors. If I move one, it just stays there regardless of key in/out of doors open/closed (unless you press one of the front arm rest lock switches of course).
* If you are doing over about 10mph, then all doors will lock. If you unlock one when your doing above 10mph, it relocks within about 5 seconds (computer apparently checks about every 5 seconds that all doors are locked if its going above about 10 mph).

Caveat to add: My alarm has been disabled by the previous owner and I dont know how he disabled it (yet). or what other effects this may have had on the locking system.
The key works (single, I only have what appears to be the master key), the locks work, but the single button on the key does jack ***** and there is no alarm function in my car. The key battery is like new condition and has full charge.
I have no idea about the immobiliser (or even if it exists on my car, but I think it does as it apparently does on the 90-92 LS400).

Addendum: If (keys in hand) I get out of my car, lock the door with the inside door armrest lock (I do that all the time) then close the door, that door unlocks (most of the time).
Most of the time? I have not found any rime or reason to it. Its ransom and I think something is slowly failing as its getting more and more often that it unlocks (unless I hold the outside handle up while closing, then it always stays locked).

Not sure if this is helpful to you (or anyone), but its helpful to me as its forced me to quantify exactly how my car behaves.