It's no doubt a big problem.  Not only did I sign up here just for this post and to contribute.  But Btc-e wont return my emails.  All though here is my story and how I got back up and running this morning.  Was up and running all day yesterday.  About 3AM I stepped away for 10 minutes to grab a drink and then come back to look at charts.  When I attempted to login I could successfully but anything I clicked would get "You are not authorized to view this page"  although I could see I had btc in account.  Also would not let trade " you incorrectly entered a value".  Then  I go to profile to try to resend confirmation, wont let me into profile.

So,  I shut off java on chrome as it is only browser I have opened since setting up BTC-e.
I restarted, ran adaware, and malwarebytes, both showing trackers.  I let them do there thing.
Restarted, downloaded Firefox, Installed addon Flash block and Quick Java to diasable java.
I then went to btce and instead of just typing in email and pass, I just clicked login and was taken to another solo login page.  After attempting to login again I was able to enter once more but this time could view my profile and and option to resend the email confirmation to verify account was there.  Before sending confirmation I went to my email associated and changed passwords.  Then went back to btce and hit the resend confirmation button.  After sending confirmation I received in my newly password changed email.  I confirmed then also changed my password in BTC-e and now I am running.  

I also think I know how I got hacked.  I was viewing the btce trollbox and was wondering were everyone is looking at live data for ltc.  I use bitcoinity for btc.  Someone replied in the box with a link to charts.  I didnt click link but copy and pasted into chrome (link looked fine nothing out of normal on outside) and believe thats how I was compromised.  Within 30 minutes me email was compromised and both my mtgox and btc-w also.  Luckily I had little funds and was able to get BTC-e back up.

I am still waiting on Mtgox as they banned my ip for 24 hrs cause of to many unsuccessful logins.  Funny thing is I have been logged in with my iphone and have been able to trade since the occurrence, yet still not able to login via computer.  Maybe I should trade them back to wallet till this is resolved.