Just did what you said, and.... it's working great with Hard Gpu Sync On.
Such a little detail, Hard Gpu Sync Frames from 0 to 1, but that made all the difference.
I've tested it with the intro of Megaman 5X (which is my reference to test this), and it's just fine!
Edit: Still a few sound issues sometimes, so I changed Hard Gpu Sync Frames to 2, and reduced the Frame Delay from 1 to 0, and now it's clean!