Well, thanks to Slithe, we have a solution for those who's saves are ALWAYS behind one step when they try to edit it.
-After you've finished playing Pokemon or whatever, save your game.
-Turn off your DS
-Start up your DS, and load another game until you get to the title screen
-Turn off your DS again
-Transfer the file to your computer, load up Pokesav, and viola, it now works
I don't know much about the mechanics of flash cards, but I guess it has some sort of internal memory, and it doesn't actually overwrite the Pokemon sav file unless you load up another game.