It would be a mistake to assume that they two systems are completely identical. The main issue, is that parts (in particular chips) can come from different places even for the same motherboard.
Also, you would assuming that all your parts are working correctly. Most computer tools don't have a good way of measuring information about what is going on hardware internally (for example, time and throughput of data going through the internal bus).
A suggestion, one of the previous posters mentioned optimal memory, and generally RAM is easy to add and remove you can try this simple experiment. Swap RAM from one system to the other and then run your performance test. If the results are different, it can have something to do with the RAM. If RAM is a problem you could swap RAM sets and test different combination's and see if you get weird results which would point to a problem with the RAM itself rather than the system.