It's not really an issue. Shonumi just noticed that some parts of SMG2 have a bigger gap between HLE and LLE than others, and he pinpointed it specifically to be graphics related. I said sort of, that it probably had more to do with the GPU thread, but you have stated that it probably actually has more to do with transfers between RAM and VRAM than anything else.
Desktop:
OS: Windows 7 64 bit
CPU: Intel Core i5 3570K @ 4.4 GHz
GPU: EVGA NVIDIA GeForce GTX 550 Ti (Factory OC'ed)
RAM: 16 GB @ 1600 MHz
Dolphin Revision:3.0, 3.0-784, 3.5, latest 3.5
OS: Windows 7 64 bit
CPU: Intel Core i5 3570K @ 4.4 GHz
GPU: EVGA NVIDIA GeForce GTX 550 Ti (Factory OC'ed)
RAM: 16 GB @ 1600 MHz
Dolphin Revision:3.0, 3.0-784, 3.5, latest 3.5