This site may be hacked

Selected answers from the Dumb SEO Questions Facebook & G+ community.

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  Hardial Singh: We are facing some hacking issues with the website nycollege(dot)edu. In Google Search Results it's coming for the homepage that 'This site may be hacked'. Earlier also we have cleaned the website and this message was removed. But now again same message is coming in Google Search Results.
  
  We have also found some unknown links generated for the website after the homepage which we later redirected to the Homepage. when we check Cached version in Google it shows some other site. Is there any tool to check what exactly is issue with the website as Google webmaster tools is not providing any details of hacking. ;
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  TEJASH D MEHTA: +Hardial Singh ;Good Webmaster is not correct place to know about hacking details. First of all contact hosting provider immediately and safeguard your site . Then use disowe tool in webmaster to remove unwanted url's
• 
  Jim Munro: Hi +Hardial Singh ;. Consider updating your Joomla version, the version you have might be making it easy for others to do this.
  http://www.joomla.org/announcements/release-news/5567-joomla-3-3-5-released.html ;
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  Hardial Singh: +Jim Munro ;we are working on updating Joomla version. In the meantime what do you suggest to remove message ;'This site may be hacked' from Google
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  Jim Munro: I am not an expert in this, Hardial, but in the times I have encountered this message persisting it was always due to an issue I had not yet found. I have not seen a false positive from this diagnostic. When I finally cleaned the site, the message was gone in hours.
  
  That said, I've been over the site and cannot see anything to indicate the type of hack. (My favourite web sniffer is off the air tonight, do you know of one?)
• 
  Jim Munro: It might be that the hack is being re-applied or there may be other types of hacks, if they can get in they usually drop more than one.
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  Dave Elliott: Run it through here https://sitecheck.sucuri.net/ it normally tells you what is affecting your site.