I'm 99% positive that the percentage of submissions graded looks like it's not based on the number of grade-able assignments, but on the total number of assignments.
Turns out, the problem was that the graded submissions counter was getting reset midway through the run through assignments (if you had a second page (or more) of assignments). Fixed.
I'm 99% positive that the percentage of submissions graded looks like it's not based on the number of grade-able assignments, but on the total number of assignments.