Hold the button in the down position and slam the door a couple times. This is a common issue, mine did it once and slamming the door while holding the button worked, hasn't messed up since. There is also a TSB for the issue....
REAR POWER WINDOW INOPERATIVE
IN CLOSED POSITION
'02 - '03 ES 300 & '04 -'06 ES 330
September 13, 2006
Some ES 300 and ES 330 vehicles may experience a condition where one or both of the rear power windows are inoperative/stuck in the closed position. Follow the repair procedure in this bulletin to install a cushion kit on both rear power windows.
^ When you receive the customer's vehicle, if the power window motor does NOT operate, inspect the system by starting with the Inspection Procedure in this TSIB.
^ If the power window motor operation is normal when you receive the customer's vehicle but the customer's complaint is the power window motor does NOT operate at times, start with the Repair Procedure in this TSIB.
^ 2002 - 2003 model year ES 300 vehicles.
2004 - 2006 model year ES 330 vehicles.
This repair is covered under the Lexus Comprehensive Warranty. This warranty is in effect for 48 months or 50,000 miles, whichever occurs first, from the vehicle's in-service date.
* Warranty application is limited to correction of a problem based upon a customer's specific complaint.
With the engine running, apply a shock to the door (by opening and closing door) while pressing the power window switch in the down direction and check the power window operation.
1. Turn the ignition ON and start the engine.
2. Open the door, and then close it 4 times while pressing the power window switch in the down direction.
^ If the above check has been conducted 5 times continuously, let the motor cool for about 20 minutes.
^ Do NOT keep pressing the power window switch for more than 5 seconds. If the power window switch is held in the ON condition for more than 5 seconds, the power window motor will stop due to overheat protection system operation.
^ If the overheat protection system is activated, let the motor cool for about 30 minutes.
Does the power window motor operation return to normal
3. Loosen the regulator mounting bolts slightly, and then press the power window switch in the down direction.
Does the power window motor operation return to normal?
1. Attach the cushion to the door glass run on the rear door upper frame.
A. Remove the rubber door glass run from the door frame.
B. Use adhesive remover to remove any grease from the areas of the door glass run that the cushion will be attached to.
C. Attach the cushions to the door glass run as shown below.
^ Cut strip "a" in three (3) 5 mm (0.2 in.) lengths and attach to the door glass run in the locations shown below.
^ Using two (2) strips of cushion, attach strip "b" along the entire length of the door glass run in the location shown below, and trim off extra strip material.
2. Install the door glass run onto the door frame.
NOTE :Make sure that the door glass run is securely fitted to the door frame and is NOT deformed.
3. Check the power window operation.
NOTE :The power window motor MUST be initialized when the power window regulator mounting bolts are loosened or the power window regulator or the power window motor is removed.
A. Open and close the power window to check that it operates smoothly.
B. Check that the AUTO UP" function operates normally.
C. Check that the jam protection function operates normally.