From this :
https://blockchain.info/wallet/features
Import / Export
-Multiple Private Key Formats - Mini private keys, Wallet Import Format, Base58, Base64 and Hex.
-Watch Only - Watch Only addresses allow you to view transactions at an address without storing the private key in your wallet.
-Brain Wallet - Generate A private key from a passphrase.
-Import From QR Code - Scan A private key using a webcam.
-Import Wallet Files - Vanitygen, pywallet, blockchain.info and multibit .key files supported.
-Export Encrypted or Unencrypted.
-JSON RPC Import - Import / Export using the bitcoind JSON RPC API
-Paper Wallets
-Sign Message - Sign a message to prove you own a bitcoin address.
-Verify Message - Verify the owner of a bitcoin address.
-Import Bitcoin-Qt Wallet - Import keys from a wallet.dat file.
So what you can do now is make a Blockchain.info account and then try to import the .key file into your Blockchain account and see if it's the same results , if it's the same result then the problem is on the file which means that that file dosen't contain the private keys for the adresses yo uare looking for .
I personally thin kthat you took the backup before creating the new adresses and receving money on them