This was posted 3 months ago, so maybe it's all water under the bridge.
I have just encountered something similar when upgrading to Mountain Lion.
The line numbers and the breakpoint icons fail to scroll along with the body of text.
I have found an (irritating) work-around. Just grab the bottom or top of the editor window and drag it a fraction of an inch.
This causes a refresh which puts everything right (until you do the next scroll).
My guess is that the change of scrolling direction convention in ML and Maveriks broke the line number code.

If you have found a real solution, let's hear it!