Well, to me they didn't fix it the first time. That is what you paid for so I would take it back and give them another chance to do it right.

When you say "center clearance light", what exactly is that?

 

Center roof light

 

So, you are talking the third brake light/cargo light??? Well, that is the most common cause of the leaking. However, it doesn't seem to be the case with OP's truck. Probably the next most common place is the rear window seal. And I am assuming the leak is in the rear of the truck. If it is up near the front, then you have the XM shark fin antennae and front windshield as possibilities.
Is your truck still under B2B warranty? As a 2013, it should be as long as you under 36,000 miles. Again, I would go back and have them fix what they were supposed to fix the first time. And if you are out of warranty, I would also argue against any further charges as well. Even if they have to redo the seal on the back window, I would argue against further charges since they didn't fix the problem and seemingly replaced a perfectly good light.

 

It is up front. I have an HD with the optional clearance lights.
Originally they suspected the antenna because it is the most common, but it turned out to be the light.
I bring it in on Tuesday to see what it is this time.

 

If the leak is showing in the same spot inside, it likely is from the same source outside. And if so, then they either didn't fix the leak the first time or they fixed the wrong problem which isn't what you paid for. I hope this gets resolved without you having to pay any more out of pocket.

 

OP didn't specify whether he paid for the first attempt.

 

Not paying for either one, I am under warranty.

 

Good

 

So, the dealer called an said the water was leaking through the screw hole. The left hole of the light, where the screw holds it to the body.
I have no idea how they fixed it, unfortunately. I let them keep the truck so they could do the frame rust TSB, so I only talked to the service advisor on the phone, and I didn't think to ask about the fix.
Thinking about it, I am a little concerned, because I doubt the threaded hole is supposed to seal anything. I would assume that the light has a leak, or the gasket does. I can't think of any other plausible answers. Unfortunately, I can think of one plausible "fix", just adding some silicone to the mounting screw. It would work, but not fix the underlying problem. I guess it would be fine, unless the light is ever removed.

I am supposed to get the truck back tomorrow, I guess we will see either then or Tuesday.