When you set the symbol -- look at the header information of the Symbol panel. There is "Symbol Color" listed. Just choose the color you want from that list.
Set your colors from the available colors panel. It will create default symbols for each one.
Open the symbol panel and click on the pin so it stays there and you can see it and your floss palette panel at the same time.
To make ONE color symbols a given color just follow this:
1: Select a color (click on it in the Floss Palette) 2: Select a symbol color 3: Select the symbol you want to use for that color.
To select other symbols/colors, repeat from step 1.
Each time you select a color for the floss, all the symbols show in that color. However, the only ones selected for change and to actually USE that color are the ones you specifically select.
To verify that the colors are ONLY for the symbols you selected, click to show stitches in symbol only (2nd option from left -- shows as a white star on pale background. Item to the left is a solid color to show stitches as blocks of color. Next item to right (star with dark background) is symbol on color background.
I think it's only designed for that purpose. Since I rarely print in color (color ink is more expensive and the symbols are sufficient), I've not noticed that issue.
I suggest you contact Mark (you can email him from his profile on this board) with your concerns. He might have a solution.