Custom colors work a bit strangely:
1) I am only able to define one custom color, even thought the color picker UI has many custom color boxes.
2) Custom color definitions don't seem to be preserved within the color picker UI. I expect that whenever I open the color picker, my previously-defined custom colors are available for use. I think they should persist across the project, and be retained when you save the project. You could even have the option of saving a set of custom colors for use in other, future projects. This would enable users to easily maintaina a commom look-and-feel across projects.
Thanks for your feedback. Agreed that colors/styles could work better as far as transfering from one IPB project to another, but for now custom colors and styles are only retained within the IPB in which they were created. To answer your #1 comment about not being able to specify more than 1 custom color --- this is probably because you have the first custom (white) box selected every timie so that it overrides whatever is currently in there. Simply select another box, it will become highlighted with a black bounding box to show you which you are working on, and "Add to Custom Colors". The box will be filled with the custom color for you to be able to use within that IPB at any time.
I hope that helps.