Exactly the flaw in the voting system I see.
I think Chris lost because of complacency. Everyone assumed he was going to be a fnalist and a lot of people voted for who they wanted to face him in the finals. The problem is that under the voting system, Chris still needed those votes.
The reason they have the voting system set up the way it is revolves around MONEY, of course. Cingular is a major sponsor of the show, and the more votes sent in the form of text messages, the more money Cingular makes from their sponsorship of the show. I think that with a vote-against system, people would pretty much call in and vote against one person, one time. With the current flawed system, people will call dozens of times or text message dozens of times in support of their favorite. So, that's how you end up with Clay losing out to Ruben, Constantine leaving well before his time while Scott Savol and Anthony Putin or whatever-his-name is continued on, and now, the biggest travesty of all, Chris Daughtry not even making the top 3. What a mess.