This only means one thing: The transactions in your wallet weren't actually in the blockchain.

But invalid transactions do not automatically get deleted after the scan,
those just wont be included to the total balance and displayed with "?" status in the transaction tab.
There must some something wrong with your wallet.dat file, like "tampered" data.

Did you actually mined those coins or have you bought/received that wallet.dat with mined coins from somebody else?