One of Projection Master's options is \C020202Shaded\C484848 Colors. This refers to pixol colors exactly as you see them: affected by material attributes and lights. With this option un-checked, transferred colors are the pure source colors unaffected by other influences.

For this option, the object should be 'primed' after dropping. Choose the Flat Color material, then use any painting brush with the M (Material only) mode selected, and ZADD un-selected, to paint the entire surface of the object.

This is also true when Projection Master's \C020202Material\C484848 option is used to embed painted materials into the texture, because the Flat Color material is disregarded when picking up.
