If you click-and-hold on a color, then drag the mouse over other colors, the selection "X" appears in all of them, but the X'ed colors aren't actually selected.
Example: Custom sovereign creation
- Go to pants.
- Click on the "Main" color box (opens Color Palette).
- Click and hold on one color, then drag the mouse across the rest of the palette. The result is below. Notice that the actual selected purple color has no "X" over the color box.

If you then mouse over the X'ed colors without clicking, the "X" disappears as the mouse leaves each color box (again, with no change to the actual selected color).
If It helps, here's the debug.err (exited without going past sovereign creation): http://dl.dropbox.com/u/8067364/Beta_2a/ColorPalette-MultipleX/debug.err