the official client gives a warning upon encryption that your wallet won't be able to be used on other machines once you encrypt it.
I'm not sure the exact wording of that, but I'm pretty sure that isn't the message.
Because the encryption process marks any addresses in the keypool as no longer being usable, the very next transaction you make will have change going to an address that did not exist in any prior backups.
When wallet passphrase enrcyption becomes enabled, any unused keys from the keypool are flushed (marked as used) and new keys protected with encyption are added. For this reason, make a new backup of your wallet so that you will be able to recover the keys from the new key pool should access to your backups be necessary.
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http://en.bitcoin.it/wiki/Wallet_encryptionI think that is what the message after encryption is telling you.