So I upgraded to CS6 and since then the stroke width tool does not seem to behave properly.
I sometimes, not all the times, get jagged lines when I try to adjust the stroke width.
Any idea what's causing this?
Looks like its duplicating profile points, but that may be entirely a precision error with your mouse clicks....
Maybe the issue is how you created the lines. blob brush, pen tool, etc. Also how many points are in those locations? The more points, the more apt it can be jagged.
I'm usually using the pen too and my Wacom. Didn't notice this issue in cs5 doing the same thing.
If the point is a curve and not a corner, make sure the handles are in the right direction, I know that is common for photoshop, but its worth checking all the same.