There seems to be a lot of confusion about how to get past PWT on DSTwo, so I thought I'd make it clear.
The DSTwo EOS automaticly patches the BW2 roms, but the patch isn't exactly perfect, which results in freezes on PWT and possibly other glitches. It even attempts to patch the pre-patched roms, which breaks the working patch.
The solution to this problem is to run a pre-patched rom in clean mode. This gives you a rom with a working patch (which won't glitch out at PWT) and tops the DSTwo EOS from breaking the patch. Of course, you will not have access to cheats or the in-game menu, but you will be able to play through the game normally.
This is what I've gleaned from reading a number of posts full of confusion and sparodic success.
FWIW, this works for me, on a 16gb class2 microSD formatted to FAT32. Occasionally I'll get some lag (presumably due to the slow SD), but it never freezes and I've played through to the 8th badge without any other disruptions.
Enjoy