I spent hours looking for the fix for the 'Jam Protection function' malfunction and found it here:
http://drivers.lexus.com/t3Portal/document/om/OM48B93U/pdf/sec_01-04.pdf
Just follow the instructions and you have your fix.
Here are the instructions:
Jam protection function If an object becomes caught between the window and the window frame, window travel is stopped and the window is opened slightly. When the power window does not close normally If the jam protection function is operating abnormally and a window cannot be closed, perform the following operations using the power window switch on the relevant door. l After stopping the vehicle, the window can be closed by holding the power window switch in the one-touch closing position while the “ENGINE START STOP” switch is turned to IGNITION ON mode. l If the window still cannot be closed even by carrying out the operation explained above, initialize the function by performing the following procedure. STEP 1 - Hold the power window switch in the one-touch closing position. Continue holding the switch for a further 6 seconds after the window has closed. STEP 2 - Hold the power window switch in the one-touch opening position. Continue holding the switch for a further 2 seconds after the window has opened completely. STEP 3 - Hold the power window switch in the one-touch closing position once again. Continue holding the switch for a further 2 seconds after the window has closed. If you release the switch while the window is moving, start again from the beginning. If the window continues to close but then re-open slightly even after performing the above procedure correctly, have the vehicle inspected by your Lexus dealer.