I'm not sure I follow your first part about acceleration. There are all sorts of different clocks, and we're talking about ones that all run at the same rate if they are at rest with respect to each other nearby.
For your second question I assume A and B started at the same place, synchronized. The answer depends on the position and motion of observer C. If C is always halfway between A and C (which would mean C still provides a nice inertial frame) then the two clocks will read the same. Other positions or states of motion of C could end up with either A or B having the lower stopped time reading. For example, if C travels with either A or C, that one will end up with the lower reading. Their explanation will be that although the other clock was running slow, it took a while for the stop signal to reach it.
Mike W.
(published on 12/05/2009)