1: Start with the ignition key in the OFF position
2: turn the ignition Key to the ON position
3: Press the rear glass control switch vent button 6 times 4: Turn the ignition key to the OFF position
5: Press the rear glass control switch vent button 6 more times
6: turn the ignition to the ON position. at this point the rear window will move up and down approximately 20mm (0.8 in). this movement signifies that the rear window glass motor has entered into the initialization mode
7: NOTE: the rear window glass control switch must be held in the UP or DOWN position until the window glass stops moving. failure to hold the switch will end the initialization operation. then the initialization will have to be re-started.
Hold the rear window glass control switch in the full UP position until the rear window glass stops in the full up position
This is taken right from the Ford Sport Trac Shop Manual for a 2001 Page 501-11-111 This needs to be done anytime the motor or switch is disconnected.
I'm having the same issue in my 2010 Limited. I asked the local Ford service guys about it last weekend when it was in for transmission work, and they said it didn't happen for them and couldn't provide any info.
Mine comes on in spurts. Several times a week, then nothing for a week. Restarting makes it go away every time.