Check your Xpub and see if the transaction is listed. If it's not listed (or if you can't check because it's not a standard wallet) get the private key and import it to a new wallet.
I have the same problem and I have no idea what Xpub is!
Xpub is the master public key of your wallet. Go to Wallet > Master Public Keys, copy and look it up on blockchain.info. You'll be able to see all transaction of your wallet. If your transaction is not there then something is wrong.