2004 Trailblazer LT - When I turn the key on I get a loud tapping noise that is coming from behind the right rear side panel under the 3rd row window. It is continues until I turn the key off
then it stops. Anyone have an idea what's causing it.

 

Sounds can be hard to trace. Are you sure it is from there? Have you put your ear against the panels?

When I first read your post I thought that perhaps it was the right-rear window motor stuck on. But then I realized you wrote it was the 3rd window.

 

I pulled out the cup holder and I can see that there is a compartment above the right rear tire well from which the loud "Ticking" is coming with a frequency of about one per second. It does stop after five or ten minutes - that time frame varies.

 

Assuming you have a Trailblazer EXT with rear HVAC (also known as the 'AUX' HVAC unit). The clicking is likely a failed mode door actuator for the rear HVAC unit. You'll need to pull the passenger rear trim panel and replace the failed actuator. I believe the part number for the actuator should be AC Delco PN 1572811 (OE GM PN 88892975).

The actuators like to break especially if you have had a recent power loss (battery disconnected for any reason or just went dead) and the HVAC system went through a 'recalibration event' where it moved all of the doors through their paces. The teeth on the gears in the actuator get weak over time and when the doors reach their stops during the recalibration event, the teeth will just shear off. From then on, the actuator cannot function properly and since they have their own feedback loop, they'll click incessantly until the HVAC control module decides to give up.

 

Thanks, that makes sense. I'll check it out and let you know.