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I am having a similar problem after adding an extra hard drive using one of the extra sata ports. Now, my fans are running at full speed.

OP: What did the geniuses say about your problem?
 
I just wanted to let everyone know that I found what was causing the fans to run at full speed. After going through the diagnostics....LED's and AHT with everything checking out fine, I found that I had a single pin from the hdd temp sensor cable that had somehow (by that I mean that I must have) been missed when I reconnected the plug. Everything is once again running smooth (and quiet.)
The fans were so loud that I didn't even want to use the computer. The fans were running around 2800rpm's and now they are spinning around 600rpm's. MUCH better!
 
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