Ram is an issue, System bus speed is an issue, Hard drive speed is an issue, OS is an issue, even anti-virus checkers are an issue. Also, even in multi threaded applications DP conigurations don't always yield acceptable results. Sometimes during some major processing, a dual system will exceed it's bandwidth, and even become slower than a system with only one processor.

For example, Alias suggests using only one processor to render with raytracing on a Dual G4 system. Even though OS X is multi-threaded, the G4's FSB becomes a bottleneck, and causes the system to render slower. Maybe that's the same issue as what you are seeing. I'm assuming not though.