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[yxalitis]

The first save always fails, it goes much too quickly, and doesn't save at all. If you restart now, you will be back at your last valid save, or worse have a corrupted save, and have to start all over again.
The trick is to save twice in a row, immediately, the second save works.
Unfortunately, you can't do this in the battle tower, or when beating the elite 4, as the game saves (once) for you, so it fails. I am training up in the elite 4, and so have to die on purpose at the final trainer's last pokemon, which takes some time I tell you! (Switch, switch, switch. Then when I am down to one pokemon, heal with 10 HP berries until finally dead!)

[cloud9x]

yep. i'm using the 2.56 patcher, and it takes forever to save but it works.

[yxalitis]

Oh! I jsut discovered, it's worse then this, it doesn't save changes made to the pokemon boxes! Store uber-trained pokemon to box, save, shut down, restart...no Pokemon.