ok I have a 2.5GHz cpu when it is idle it runs at 1.25GHz while running boinc it still runs at 1.25GHz I assume this is because of the nice level so at what nice level will it start using all 2.5GHz? and how do I set it permanently?
I'm running Ubuntu 8.04 and Boinc 5.10.45

You only have one CPU, right? And it's a single core CPU?

Going by your story, I assume that your kernel thinks it's a dual core CPU. Where one core isn't working. When you reboot, what does the BIOS say your CPU is capable of? When you actually go into the BIOS, is your multiplier and Front Side Bus speed set up correctly?

Depending on the pin package, the AMD Athlon 64 3200+ runs at 2.0GHz (939 pin (FSB/multi = 200/10)) or 2.2GHz (754 pin (FSB/multi = 200/11))

Your benchmarks are also weird, being at 1,000 mflops for both integer and floating point. Are you overclocking? Did you download BOINC from the BOINC site, or through your package manager?

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Locate a file called cpuspeed. It should be a text file somewhere in /etc. Look for a line in the file (use a text editor) that says:
IGNORE_NICE=1

Change the 1 to 0. Restart your system.

I haven't installed Ubuntu 8, so the steps may be different. If there's anyone who knows Ubuntu better, perhaps s/he could clarify my directions.

Also, that utility that shows your the CPU speed should also be able to change it. Try changing your CPU speed yourself.