I was having the same problem and it was driving me a little nuts. Fortunately, I do a lot of scrolling using the trackpad, but sometimes I really want to just hold down control-n to scroll through a bunch of code.
I just discovered if I close the sidebar (that's what I call it) everything is fine.
So that got me thinking because I installed the Soda theme on my MacBook Pro.
I disabled it, and my key repeat rate is now the same as the system-wide setting.
So I suggest not using any themes and see if that clears it up for you.