ok so first i built my mom a micro atx computer. it isn't super small like a shuttle, its a mini tower. anyways, with stock heatsink it was getting 50C. I decided I needed to upgrade.

Let me tell you one other thing quick. I also just built myself a system with an x2 5600+. with stock heatsink it got 50C idle. With Arctic freezer 64 pro it got 35C when OC'd

ok so I figured for my moms computer i'd also get an arctic freezer 64 pro to bring her temps down. Well I installed it, I just used the thermal pad which was on it. It was getting 50C. I was like wow what. So I removed it, cleaned it off, and reapplied it using arctic 5 silver instead.

With the arctic 5 silver, still 50C about.

I don't understand this. Yes the computer has poor airflow becaues its a micro atx, but shouldn't the arctic freezer 64 make a difference over stock. It sure made a difference in my other computer. http://www.tabsite.net/TabsBuild.JPG

Sounds like the case doesn't have sufficient airflow so all the cooler is doing is blowing hot air onto the processor. What's the temperature like with the side of the case removed?

Its the case. I've got one just like it (M -ATX mini tower), are there any side / front inlet fans pushing fresh air into the case?
I cut a giant hole in the side and am ready to fit a piece of car modding mesh I got from Halfords on the side. You can then tyrap a case fan to the side on the mesh if you like.
It got very hot so hot that when a game was played the GRFX card would get so hot it would turn into a slideshow, the northbridge got very hot too. This is with stock settings.
(not my main rig).

How hot is it getting under 100% load? If it's under 70°C then it's probably the automatic fan adjustment that's keeping the idle temp at 50°C. Don't worry about the temps except if they exceed 70°C.