Not going to be able to help but do provide a little more information.
I have a cab also
when you put the top down the windows go part way down, when the roof is stored, the windows go all the way up (yes dumb) - what does the rear window do?
When you put the roof up, the windows go part way down and stay there - what does yours do?
windows not closing when roof is closed.......windows go up but then one goes back down. - is that when you use the switch. Does it do the same thing from the door switch and the master in the center console?
When the engine is off and accessory power is on, the windows are not auto (one touch up). Does the window go up then down?
Software update - Assume you went to the dealer. They have no ideas?
I have a cab also
when you put the top down the windows go part way down, when the roof is stored, the windows go all the way up (yes dumb) - what does the rear window do?
When you put the roof up, the windows go part way down and stay there - what does yours do?
windows not closing when roof is closed.......windows go up but then one goes back down. - is that when you use the switch. Does it do the same thing from the door switch and the master in the center console?
When the engine is off and accessory power is on, the windows are not auto (one touch up). Does the window go up then down?
Software update - Assume you went to the dealer. They have no ideas?