There are a few issues here, one of which I have been planning on submitting a feature request for.
A common duplication occurs when you make a slight RGB adjustment to a color in a model that has already been saved and you are now working on the next version. You will see the same custom color name you created in 2 versions, the new version with an added number suffix (if you happen to leave some of the unedited custom color in the model).
If this is not the case with your model, maybe there is a further CMYK to RGB complication?
Even in RGB mode, color edits do not stick precisely, they modify by a point up or down in my experience (on Windows).
The other issue I have found with custom colors is that you can’t have 2 colors with the same RGB settings and different names (important in certain render situations - ex. if you need the same color with gloss and matt finish areas in a render).
All this seems to point to some kind of software issues with color, maybe there needs to be more detail to cover all eventualities?