So I've had no problems with PokeShifter,and before you ask my SoulSilver is Japanese. But after patching Black with V2, I can't for the life of me get PokeShifter to work. The DS that downloads the program that has my Japanese SoulSilver in it goes to the Black Nintendo screen as usual, but then it freezes and Black version exits Pokeshifter mode.
TL;DR: I think V2 may have messed up the PokeShifter.