That Kouye has opened a whole new window on the Bitcoin world for me, I just tested those commands on the wallet open on this PC and can see what you mean. This is my Windows PC so this wallet contains very little, as the wallet I'm talking about has a lot in it I only load it on my Linux Laptop when its offline and take a peek. I will do this tomorrow. I think you have given me enough information to help find the cause but its not sure because the 40mBTC transaction is actually missing. I really didn't know that command window existed and I will enjoy exploring that.
KieranJones1, I don't quite understand your reply as this is a Bitcoin-Qt wallet. In this case I only used Blockchain.info to check the address concerned to find all the transactions going to my address. Six transactions exist on the Blockchain, only five transactions exist on one of the wallets, six on the other.
Thanks Y'All