This was part of my first attempts to bring Audio Capture into Papalotl.exe.
Eventually, with more knowledge and experimentation, learned that my CPU was too weak to maintain both streams in sync.
Issue got resolved by separating Audio and Video into two capture methods instead of 1.
Contra 3 was my benchmark, now is Dolphin running at 60FPS in a i3-2120
Oddly enough, reducing the bitrate fixed it, which is lower than what WASAPI outputs by default.
Eventually found a solution to this as well while maintaining WASAPI default bitrate.