Do you have resources and work loaded for each task?
%WorkComplete=Sum of (%WorkComplete)*(Work for one task) for every task
below the summary line, divide that sum by the total of all work on the
summary line.
Of course, project does this for you as long as there are resources assigned
and work assigned.
One other thing to look at, examine the earned value methods utilized for
each task. Make sure they are all %Complete not Physical%Complete.