The boxes already show a different color in the 2Dview so it's not surprising they also show different in the 3Dview and renderings.

I tried it with two boxes: One box, white, mat. Copy/paste and place side-by-side. They show as a single, longer, box because they have the same color in both views and renderings.

Are you absolutely sure both boxes have the exact same color and shininess?
Did you add some lighting that could possibly touch one box and not the other?