[Shadowcat]

Firstly, my apologies. I was confusing mission type with sector size.

Secondly, the modd thing just shouldn't happen. The game keeps completely separate high score files for each mod (the information appears to be stored in the mod's game.cfg file).

You haven't copied the game.cfg from the default game into a mod directory have you? (or vice versa). That would explain pre-existing scores appearing in the wrong place.