ugh, that doesn't sound too good. I think it may actually have something to do with the way FS calculates kills for awarding ace medals; if you go straight from under 60 to 150 or higher, it may end up getting confused and doing some strange things. (the Volition people probably never anticipated that missions with 91+ possible kills would exist
)
I actually lost all of my custom table files (intended for my campaign) when installing Twilight; I think Kazan's installer overwrote the ones I had in there. Since that time I have always kept two or three backup copies of the missions and mods (tables/effects/etc.) just to be safe...