They are special legendaries like Latios and Latias... Diaruga should be in Pokemon Pearl, and Parukia should be in Pokemon Diamond, This is my thoery:
It's always closing to the opposite.
P = Pearl/Parukia
D = Diamond/Diaruga
So they mix them around to spice up the games a bit.
D = Diamond/Parukia
P = Pearl/Diaruga
Again just my theory.