@fmjason,
The colorSet seems to be working fine irrespective of 3-digit or 6-digit hex values.
Also in JSFiddle shared by you, the first two colors in the colorSet are almost similar because of which color of both the line series look almost similar. Changing the hex values in colorSet(try colors with a significant difference) should work fine in your case.
—
Shashi Ranjan
Team CanvasJS