I've had this issue with the one-touch feature (auto up and down) on my power windows since I swapped out my manual windows. Auto-down works fine, but auto-up goes all the way up and then back down about halfway, as though the anti-jam safety feature is activated. There are many threads about this issue, and one recommends the following instructions from the FSM, which I tried.
I took the motor out, ran it continuously for over 4 seconds, and re-installed it without moving it. Still not working. Any help? None of those threads I mentioned had any solutions.
__________________
‘98 T100 SR5 4X4 5spd (sold)
‘99 4Runner SR5 4x4 5spd E-Locker Unicorn