Seems you keep typing. Like posts for Titans, I too was washing the vehicle and noticed brown in the rain channels. I thought it was dirt but no it is rust.
So not just Titans but other vehicles as well. With all of these complaints nothing can be done?
I cleaned mine really well, cleaned the channels with alcohol, taped off around them, spray painted gloss black. It's not perfect, but you'll only see it if you're looking for it. No one else is looking at the top of my truck anyway except for maybe semi trucks.