Since you bring it up, let me explain a bit about what ColorThink Pro is doing in the “Extract Unique Colors” function.
First of all, we should remember that individual RGB values do not necessarily equate to being distinguishable colors. Having 16 million color combinations does not mean that each of those individual colors will be perceptible by the human eye. For more on this, see Color Management Myth number 28 from one of our newsletters:
<http://www.colorwiki.com/wiki/Color_Management_Myths_26-28>
When you choose to extract unique colors in an image in the CTP worksheet, CTP will convert the image to Lab space, and then round the result with a somewhat coarse rounding. This is done on purpose to optimize these colors for graphing. You will probably get fewer unique colors than another method would give you.
It’s nice to hear what features you want to see in this software. If this function does not do what you need, go ahead and fill out a feature request ticket, and we’ll look into putting this into a future version of ColorThink. Make suggestions, like “install a checkbox for ‘Do not constrain unique colors’” or something like that.