CPU overheating

I just finsihed building a new computer with a MSI P55 GD65 mobo and an intel i5 cpu. The idle temp is around 40c but under load or when checking the bios it gets between 70-80c. I have an Antec Nine Hundred Black Steel ATX case with 2 front fans a back fan and a top fan. The bottom front fan is not plugged in but that should not cause this much overheating. The power supply, graphics card (GeForce 9800 GTX) and aftermarket heatsink (Scythe Ninja Mini Rev. B) all have running fans. All case fans are set to medium. I would like to know where I should start looking for issues, and also if it is ok to take off the heatsink to see if it attached correctly (smudged the thermal paste). Also, the GPU and CPU are pretty close, I was wondering if it would be better to put the GPU on the other PCIE slot that is farther away (does it matter which slot the GPU is in?). Thanks!
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More about overheating
  1. Check your manual, but the PCI-e slot closest to the processor should be the one to use. As far as heat, do the simple things first; take off the side panel of your case and see how it affects the temp, try setting the fans on high, look to make sure your CPU cooler is at a 90 degree angle to the processor so the parts make full contact, etc. If none of that makes a difference you can remove your heatsink. Just be sure to clean both mating surfaces thoroughly and reapply your thermal paste when you put it back together.
  2. When you say the CPU cooler, do you mean the heatsink? Thanks for the reply, I will try taking off the side panel to see if that helps.
  3. Reinstall the heatsink. Don't forget to clean up the surfaces (both cpu and heatsink) first then apply some thermal compound.
  4. Yes, the heatsink. Some of the models are tall with the fan assembly attached and have springs that provide the pressure holding it against the CPU. It's easy to bump it off center and lose complete contact against the chip on some of models.
  5. This aftermarket heatsink has the fan seperate from the heatsink. I can attach it to any of the 4 sides. When I put the heatsink in it was level, but I will check that again to see if it still is. Would that explain how my temps are cool when I am not runnning anything but they are hot when I have it under load?

    I did put in some thermal compound when I first put it together but if nothing else works I will try reinstalling the heatsink. What should I use to clean the surfaces if I need to?

    I should have some time today to try some of these things out. I will update this when thats done. Thanks again for the responses!
  6. Well I ran the computer without the sidepanel on. The initial temp at the bios screen was around 35 c, instead of 70-80c, but if I left it on the temp started going back up to around 70. It was much slower then before, but still nothing that I would like to operate at.

    The heatsink still seems to be level, but I can't tell any more then that.

    Do you think that I have the fans improperly placed, or do you think it has more to do with the heatsink? I am still kind of confused at how it can sit at 40c idle all day but when I look in the bios or run a game it jumps up so high.
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