I had this problem using cIOScorp with a backup disc. Running it through a backup launcher (and having it use cios249) seemed to fix this issue. It also appears that DARKCORP fixes this issue as well.
Use this to open the AFS archive:
http://code.google.com/p/puyotools/
That should be able to view the AFS archives fine. AFS Explorer seems to give a lot of problems with newer games.
This version no longer gives you a loss if the other person disconnects on wifi (previously both people would get a loss if someone disconnected). It also includes a new mini game called Puyo Sniper, although no one has figured out how to unlock it (or if it is meant to be unlocked at all).
I can confirm that this release works.
The controls for this game don't really seem to be as bad as everyone says. Sure, Nintendo should have left in the option to play with a Gamecube controller, but the Wii controls work ok.