Jonathan, I hope you don't mind an outsider's theory on this.

There's a couple of reasons why the lower mhz machine does more work. Your AMD is probably producing higher Gflops, thus producing more work. I'm surmising the Intel is probably a D960 processor. The D series, although being a dual core processor, does not produce high Gflops. Certainly less than the latest C2D processors. If you are using BOINCView, you can check the rating of each machine in Gflops.

Do you use your desktop machine as your main machine? Any other programs you run take away from your crunching output, but I would bet it's mainly the difference between the AMD vs Intel output.

For example: I have a D925 3ghz dual core which only produces 1.6 Gflops. Compare that to my E6750 C2D (overclocked to 3Ghz) which produces 2.9 Gflops. That's a major difference.

Exactly. Which is why I asked for the full specifications. GHz power is important, but it also depends on the type of CPU. Pentium Duo Core, Core 2 Duo, Core 2 Quad, Pentium 4, Celeron, etc. I'm not to familiar with AMD. I'm an Intel/NVidia person.