What mobo? If you are using a 200 series mobo, I believe there's an AVX offset in bios. If the benchmark uses any AVX whatsoever, the cpu will automatically downclock the offset amount. Base clocks are read as part of the cpu-ID, they are factory set, but since turbo speeds are variable it might be reading your turbo minus offset.
Base speeds are only used upto @ 30% loads before turbo kicks the cpu up, so since the benchmark is using 80-100% loads, it's not actually measuring base speeds, just turbo speeds. It's also possible that the cpu is thermally throttling under the benchmark usage, dropping you down to 3.9GHz under such a heavy load.
Hard to say exactly why since nobody but you can see the conditions and restrictions you have in place.