The E brake on my nx has gotten to the point where it doesn't disengage anymore(frozen caliper pistons??) so I just completely stopped using it. But the brake handle on mine goes down without a problem the only problem in my case is that the brakes don't release. Try spraying some WD40 on the rear calipers and hopefully that noise wouldn't come back.
I dont know too much about brakes so this is as deep as my knowledge goes

Good luck,
Nick