One solution I used to help my situation when I was using a trio of gtx480's was to place an exhaust fan on the case side right next to the rear of the GPU stack.
This actually helped quite a bit because it pulled much of the heat away from the video cards instead of allowing it to rise.
I think all cards were ten C' cooling with the fan in place. It wasn't anything crazy. Just a typical 1400 rpm sub 60 cfm fan. But it helped a ton.
But to answer your question on why the CPU fan is behaving that way it may be due to the bios fan control programming. Such as if it has a light load but can sense a lot of heat in the remainder of the components. If its detecting a high temp on the board one of its conditions may be to max the cpu cooler to prevent others from overheating.
@Boinker - What do you mean by leaving the louvers in place? You mean the front grill with the bars? I wanted to open it up and expose the fans more. I was able to keep 2 of the 3 3.5" bays available while still fitting in the 2 120mm fans which is a win. I could put another 3.5" device or extra hard drive if I needed to. The case itself is just a classic. The biggest problem with it compared to today's cases is the lack of any real way to do decent cable management and the fact it comes with 5 x 80mm fan spots. Upgrading them to 2 x 120mm in front and 2 x 92mm in back really helps airflow and being able to use bigger, quieter fans (which reminds me I will be replacing the fan in the hot swap bay since it's the loudest thing in the case.
Yes the grille bars. I thought it would look wrong in my case but It was done in style on your part. I lost both my 3 1/2 bays. the intension of my mod was to mount water cooling internal of the case. And it worked out. just have not got anything in it as it seems I only have one system at a time. lol. But in other news its nice to see another modded dragon. thats for sure.