Generation V:
Doom Desire no longer uses the Special Defense stat of the targeted Pokémon, but instead the Special Defense of the hit Pokémon.
Quoted directly from Bulbapedia.
Unless Bulbapedia is wrong... Gen V has changed this, and it now calculates damage with the SpD from the hit Pokémon, in this case Scrafty.
But seeing as I can give no other explanation to the Scrafty-Jirachi theory, I'll have to guess that Bulbapedia is wrong?
EDIT:
Same applies here.
According to Bulbapedia, it used to apply to Future Sight as well.
But, once again: I read this on Bulbapedia.
Generation V:
Future Sight no longer uses the Special Defense stat of the targeted Pokémon, but instead the Special Defense of the hit Pokémon.
Can anyone confirm whether Bulbapedia is correct on Doom Desire and Future Sight or not?