Obviously the same password was not used on both email and btc-e, or the hacker would have been able to withdraw the funds.

I deleted previous thread because I wanted BTC-E to not get pissed.

I've recieved a response from BTC-E now asking for verification which I have provided. As long as everything work's out I will have nothing bad to say about BTC-E, and continue using the exchange as I have for the past 2 years.