The running weighted total is based only on scores that students have gotten in the gradebook vs. a weighted total which is based on all items, graded or ungraded, in the gradebook. (In either case, you need to tell Bb to calculate certain gradebook items into the running or weighted total. )
For the running weighted total to work properly, you need to have a grade entered for all students even if a student did not receive credit for a particular item. If, for instance, a student missed taking a quiz and will not be allowed to make it up, s/he has a dash entered in the gradebook; you will need to go in and manually put in a grade of "0" for that item so that Bb will calculate the running weighted total properly for that student.