What are the wire colours going into those plugs? It looks to me that someone has replaced the window motor with an aftermarket one and that's their attempt at splicing them in... you mentioned 'Window not set' messages to me, which if that is the window motor, then it looks like there are sensor wores coming out of it to the long flat plug - which is going nowhere, so the BECM won't be seeing an input on the anti-trap feeds, and thus won't set the windows.
I wouldn't be able to tell if those motors even have sensors that are compatible with the BECM without knowing more about them - but if they have been replaced in EVERY door, then it will explain you not being able to 'set' the windows pretty simply!!
From what I can tell, they have spliced the 2 thicker blue wires into the feeds for the motor from the outstation, and left the rest alone.
That 6 way plug with the yellow insert is what SHOULD be plugged into the window motor, if it were a genuine P38 one...
The good news if you want to swap them back to being original is that they aren't that expensive second hand as they hardly ever fail... the bad news is that the replace them you ould need to take the window regulators out. Though on second look, it appear the regulator is aftermarket aswell - as it's definitely not the LR shape... again the proper ones aren't expensive - just annoying to (probably) have to change all four...
If the windows actually work properly other than not 'setting', I'll try and find some info about the window motors and see if there's a combination of the wiring that's there from the inbuilt sensors to see if they will trigger the BECM properly.