I'm using a custom art brush I made with the pen tool, and the stroke seems to have a different colour than the fill and I can't figure out how to get the stroke colour to match the colour that is shown when used.
Color variations in the brush would be caused by the Hue Shift setting in the brush options:
Hue Shift does some color "voodoo" I can't really explain... it combines the stroke color (brush color) with underlying colors to come up with an overall "shift" between the two. I don't know the exact math or logic behind it. However, I have always found "hue Shift" to be terribly unpredictable in most instances. It's okay if working on a fairly monochromatic area and toying with it to see how things shift (then adjust).
If you want the color to change with the applied stroke color.. set it to Tints or Tints and Shades, the latter is my personal preference.
If you want the brush to remain the color it was created at.. set that option to None.