Clicking Rear A/C
I think I know exactly what you're talking about. It happened to my '03 Expedition... three times. I first noticed it when I went to switch the rear A/C from panel to floor. A clicking started from the cargo area. The blend door was stuck. The dealer replaced it under warranty. 5,000 miles later, the same blend door went out again. Dealer replaced it. The third time, I went to move the temperature switch from cool to neutral. The clicking started again. Only this time, I was 1,000 miles past the factory warranty. The dealer determined that it was the temperature blend door this time and replaced it under their "good faith" warranty program. I lucked out because they said the repair would have been $80 for the blend door and $420 for the labor (they have to disconnect cooling lines, remove the rear A/C system from the truck and take it apart to reach the blend and vent doors.
If you hear the clicking when either the blend door or vent door is in a certain setting or position, but stops when you turn the dial or control another way, you can be fairly certain that the problem is a faulty blend or vent door.