Starwars.com confirmed they used a black R2 for bluescreenshots. The mystery is solved!
I know why he was originally black, my question is why would they fix it in Jedi and Empire, but not fix it in ANH? I think it was an oversight. In fact even "Darth Editous" with his spectacular upgraded addition seems to have missed this. (That is not meant as a criticism), He caught many things the LF guys did not and some things I didn't even know about.