What webmaster tools shows and what google analytics shows are always different things.
Where you might be getting confused is because you are accessing webmaster tools IN your google analytics (they can now be hooked), doesn't make webmaster clicks any more accurate.
Use your actual google analytics and if there is still a problem then maybe there is not much traffic for that keyword or as others have said fix headline and description.
P.S. Also check you are ranked number 1, not just shown that as a personalised result by the big G.