Sorry the program is giving you problems. Does this bug occur with every planbook file that you create? Does the bug occur every time that you try to apply changes in the update courses window?
Could you do me a favor? Create a new, empty class in Planbook and send it to me before trying to change colors. Perhaps by looking at the file your version of Planbook creates I can track down the problem that you are having. My email can be found easily at: http://www.hellmansoft.com
I'd also encourage you to join the Yahoo Group listed above as it's often a quicker way to get help if you need it.