Check for these things: Does your Metamask have more than one account associated with it? Are you on the Main Network? If you have tried all this, I would recommend using the Mnemonic Phrase you got from Metamask when you click on the little key and then use it in Myetherwallet to access your address. Then you should be able to move your tokens around without Metamask.
RE: How to Free EOS Tokens from Metamask and other issues