Hi,
2 boards using the 5V and the 3V? The regulator depends on the 5V ground, if I've understood correctly? So the 3V is a "child" of the "parent" 5V or whatever you want to call it? So you shouldn't need an additional ground cable, I think, because surely the regulator ground is the same potential as the 5V shared ground, as the regulator ground is the original 5V supply ground, so both boards share the same ground, regulator or not.
Another matter may be how the 3V cabling from board B to A may need to be done, I'm not up on shielding and so on.