When I compared in WinMerge the only difference was the last modified date.
Yarr. The player's last loadout is saved in the campaign file, and is always restored when he replays the most recent mission. When he plays a new mission, or a new version of the old mission (as determined by the modified date) the loadout is wiped and reloaded.
Taylor's new pilot code will fix this, but it's a rather significant gotcha to watch out for. (It's also a problem if you're testing a mission you're FREDding, and you're using a non-default loadout, as the loadout will be reset every time you save the mission.)