The red box contains:
1. The Phantom Menace (DVD + Bonus Disc)
2. Attack Of The Clones (DVD + Bonus Disc)
3. Revenge Of The Sith (DVD + Bonus Disc)
The blue box contains:
1. A New Hope (Disc 1 is the 2004 edition, Disc 2 is the 2006 edition)
2. The Empire Strikes Back(Disc 1 is the 2004 edition, Disc 2 is the 2006 edition)
3. Return Of The Jedi (Disc 1 is the 2004 edition, Disc 2 is the 2006 edition)
So to answer your question, the blue box contains both the 2004 & 2006 versions.