OK, the latest
OmniFocus sneaky peek build has a workaround in place: if it sees that a rich text clipping has a background which is entirely black, it ignores the background color rather than applying it to the note.
(The rich text clipping that we're getting sent has black text on a black background. My guess is that the black background was originally completely transparent, but the transparency got lost in converting to RTF because RTF doesn't support transparency.)