How come I'm getting a lower 3DMark when I'm overclocking?

Score using Intel Dynamic Platform & Thermal Framework running @ 3,896 MHz = 12747

Score using Intel XTU overclocked to 4.1 GHz on all 4 Cores = 12732

How come I get a lower 3DMark using the same driver despite the 300 MHz increase and on all cores?

Here are my XTU settings:

 

You must look at physics score. Your benchmark test with xtu have higher physics but lower graphic score. This is not a cpu problem. Do the benchmark tests again and repeat same test after reboot. Only difference You have is lower graphic score. Run also 3Dmark Fire strike.

 

You can run Hwinfo64 in the background and after the test is finished see if the processor had Trottled in the test . You can also use 3Dmark11 in window mode and see Hwinfo64 simultaneously in real time. Other option is to use Hwinfo64 and Rtss to monitor processor and graphic with osd in real time during the benchmark test.

Edit: Set up the comparison such as the link when you want to compare the results. It gets a little clearer for you then. http://www.3dmark.com/compare/3dm11/9865079/3dm11/9865377 It's smart to write a comment in the "Description" in your benchmark result details in 3Dmark.com. So you know what changes(overclocking) you might have made on the processor/gpu or in the os.
With your 4.1ghz on all cores should the physics score in 3DMark 11 have been closer to 9,900-10,000 points when you use Win 8.1. With 4.2ghz = 10100-10200 and 10300-10400 with 4.3ghz. Recommend running some pure physics tests in 3Dmark11 and Fire Strike. In 3DMark Fire Strike should the physics scores be about 11650 with 4x4.1ghz... 11,800 to 11,880 with 4.2ghz and 12000-12100 with 4.3ghz if everything is ok. All this 3Dmark11-Fire strike physics scores is tested with Win8.1