I have recovered the coins so luckily for me this is not a problem now , it's just that I don't understand why not all the addresses are shown in the bitcoin client. This is a big problem if I would like to create a paper wallet with many wallets, as I am afraid I'd lose some on the way, no? and the fact that not all the coins are showing up on the blockchain, could also be a pretty scary view.
You should not be messing around with the private keys of a wallet if you don't understand the technical details of how your wallet works.
Bitcoin-Qt only shows in the "Receive" section those addresses that you have chosen to create for the purpose of receiving new transactions from others. It does not show change addresses that are created with every transaction that you ever send. This is a design decision made by the creators of Bitcoin-Qt. For the MANY people who have NO understanding of the underlying technology, and just want to be able to send and receive bitcoins from a computer program, showing change addresses would add confusion and unnecessary complexity to the user interface. It is expected that if you are going to be messing around with the debug interface or the RPC interface then you should know what you are doing, and understand how the wallet works first.