Load flags are a set of two hex digits, starting at 0x80AD8B98, which have a diverse range of functions attached to them.
These bits seem to be unused.
If not set, the game will load the Motion and Etc files separately from each other.
Seems to be used by Olimar and IC's for something physics related.
Seems to be used by DK, Luigi and Peach for something sound related.
If set, the game will try to load a FitXXXFinal.pac file, and will prevent you from using a Final Smash if the file is not found.
If not set, the screen tint that occurs during a Final Smash stays until the end of the FS sequence, regardless if you die during.