You were just given exact instrucitons.
In bitcoin-qt, the menu option Settings->Encrypt Wallet
There is only one step (other than follow the prompts and enter passphrase twice).
The reason why your new wallet isn't encrypted is ... because you have never encrypted it.
As to why I secured the encrypted wallet, that's another story.
You can see how including it in your description complicates the situation with uncessary details. In the OP it almost seems like you expected the new wallet to be encrypted because the old wallet was encrypted.
This new wallet.dat is completely independent so what you did or didn't do to the old wallet.dat has no relevence. For all intents and purposes the client has no knowledge of the old wallet until you restore it (if ever).