When applying to a couple airlines I finally realized that my TT didn't equal my MEL+SEL, and my MEL+SEL didn't equal my day+night, which also didn't equal my TT. After a lot of searching and head scratching I found the errors (three of them, all stupid math errors, mostly on flights that ended late night).

As ridiculous as it sounds, after every page now I add SEL+MEL-day-night and if it equals zero, I feel a little better about it.