In both scores, was the system set to use the XMP profile? If so, then the measurable difference between the use of 2 vs 4 DIMMs slots has been mixed in with the changes between the RAM speed and timings. If you can spare the time, try running the tests again, with the new memory kit, but between each run alter the number of DIMMs used - I.e. start with 1, then go to 2, etc.
Unless you only alter one variable in a test, you're never going to be able to tell for certain that the experienced change in performance is down to the aspect you're hoping to analyse.
Edit: It's worth being a little cautious when using 3DMark to compare changes that result in just a few % difference. Here are 3 runs I did this morning:
www.3dmark.com
There's a 6% difference between the lowest and highest CPU results, and yet the only thing between each run was rebooting the PC.