Was the book by a guy named Hankock?He appears to have done much of the research into the link,I've read of the theory being dismissed also though,mainly due to the size,they say that Malta is to small to have been Atlantis(how they work that out if most of it's submerged I'm unsure).
The other reason is that they say Malta has never been completely submerged.There's lots of links on this but I don't know if you've seen this one,HTH.Regards,Hobby.
http://www.timesofmalta.com/core/article.php?id=113731