Hey, I've got the same problem pretty much. I assembled my computer not so long ago, and after some test, i found out that only one of the core is doing the work. (I also got Athlon 3.0 Ghz 6000+)
Even with the game Supreme Commander, which is supposedly dual and quad core compatible, it doesnt do anything. One core runs full, and the other about 4%. Temperature could be an issue, but i manage to keep the temp below 50°C.
I've got a 8800 GT 512Mo and 4Go of RAM (kingston) with Win Xp 32bits.
I wonder if my power supply is a factor(500W), or if the motherboard could be an issue as well.
I've got an ASUS board and ASUS video card.
I've got nothing overclocked, since I'm not an expert in this.
Please help me, cause so far, I'm not seeing much difference from my previous settings:
AMD 2.4Ghz 3800+
7900 GT 256Mo