Looking over the character sheet again I think there is still something wrong with the skills. I still count 36 points spent. With 40 available that leaves you with 4 unspent points. I think the problem may be that the character sheet incorrectly labels Knowledge:Local as a cross-class skill for her. This might lead the program to count those 4 ranks as 8 points, but it actually is a class skill for a Rogue, so should only count for 4 points.