Hmm. I don't own MGS, so I can't test that out, but I'll test out SMG (since I have a completed save file). I'll report back on that. Until then, someone else can help you, because I don't know if I can do much more troubleshooting until I can get that done.
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