I pulled this from the Dolphin Wiki for Arc Rise Fantasia:
Might be a speed issue with your hardware; overclocking would probably get the audio and video to sync. What's the exact CPU model in your computer?
Also, Audio Throttling can be found in the Framelimit option (from the first screenshot you posted). To enable Audio Throttling, just set it to "Audio".
Quote:Runs between 98% and 100% with D3D9, no noticeable slowdown in game, but cut-scenes lose progressively sync with their audio (regardless of Dolphin setup). Overclocking the CPU to 3.4GHz solves the issue.
Might be a speed issue with your hardware; overclocking would probably get the audio and video to sync. What's the exact CPU model in your computer?
Also, Audio Throttling can be found in the Framelimit option (from the first screenshot you posted). To enable Audio Throttling, just set it to "Audio".