How do I recover Bitcoins from a Change address that is in a corrupted wallet?
If that really was a change address, its private key is included in your backup of the wallet, even if you can't see it in the client GUI; this is because Bitcoin-QT always keeps some (a hundred, IIRC) precomputed addresses ready, and uses them whenever you request a new address or it needs a change one. However, change addresses are never shown in your address list, so you couldn't see them even if this was your original wallet.

If those Bitcoins have really been sent to a change address, you'll still see them in your balance, and you'll be able to spend them. However, if your balance is actually less than before, then they'we been transferred somewhere else, thus the trojan hypothesis sadly applies.