Glad someone found this thread. Mine does it too. I've been meaning to search on here to see if this had come up before.
My inspection is due in a couple months, so when I take it in for that, I guess I'll have them check out the hissing brake pedal as well as the rattling sunroof.
This is kinda strange. Toyota has an incredible reputation for service / quality. But it amazes me how many things come up that just don't seem to get addressed.
My '99 only had one annoying problem, and that was a creaking / squeeky clutch pedal. It would get to the point where it would sound like the entire thing had rusted, and was about to brake apart. That started at only 6 months of ownership, and never went away. Had it replaced several times, nothing they could do.
Now the new ones seem to have some seat issues, sunroof issues, brake pedal, etc. It sucks when you take it in to have the seat fixed, and they just tell you there's nothing they can do, and Toyota has no fix for it on the horizon.
I love my Runner, no question about it. I just wish Toyota would fix some of this stuff.