Thanks for the response. I've actually tried all the different preferences, with no success. Also, I have about thirty of these Media100 generated color clips, and editing each one individually wasn't my favorite option. Maybe the folks at Media100 can add this preference to the existing replace media procedure.
You're so right! Replacing M100 Color Generated Clips with another one just doesn't work.
I just tried something: go to Photoshop, create a new file -format matching your Timeline's-, fill with the desired color and import this color file into a M100 and use it as Cmd+Drag+Drop Replace feature. It should work.