This is kind of like my weird lighting 'feature', only much more annoying. If you have a prim with each face set to a different colour, then try to change the transparency setting for the object as a whole (all faces) using the Transparency box in the edit window (ie. not via a script), it will immediately change the colour of all faces to match that of the primary face (face 0).
Obviously, this could get very irritating.
