This is mainly because QT wallets have a default pool of 100 pre-generated addresses (the 100 next addresses it will use as change or show you when you click on "new address" are pre-generated). Each time you use up an address from that pool, QT creates a new (random) one to keep a 100 pool.
So if you clone a wallet to another computer and use both, you'll have the impression that they are syncrhonized, until you reach the point where you used up all 100 addresses from the "common" pool, and they begin to use random address from the "fresh" 100 pool each one will have created on his side.
What you are doing here is different. You just backed up a wallet, and created a fresh new one, not expecting that they behave the same way.
So don't be afraid about that warning.
Also, you cannot specify the wallet.dat filename when running QT, so you'll have to rename/copy/move your new wallet before copying back the locked old one (and renaming it wallet.dat if necessary), before next password cracking session.
To learn more, you may simply search in this sub for material about QT wallet.
I haven't backed up my wallet yet, because I am afraid I will mess it up.
Also, I have noticed that my wallet just closes itself, and when I re-open it, the block chain sometimes does not show on the bottom of the interface. Like, the interface does not always show the green bar which shows status of syncing.
Thanks