I have not experienced any sort of audio problems with Midway Arcade Treasures...Do you have your GameCube audio hooked-up to a receiver or are you listening to the audio through your TV? I do sometimes notice a delay between the audio on the TV and the receiver (with the receiver being on-time and the TV being a fraction of a second behind, creating a reverb effect).
In an unrelated, related question...Has anyone experienced audio problems with True Crime: Streets Of L.A.? I get an annoying amount of static over a few of the songs during menus and driving sections of the game. The static is loud enough to drown out most of the song, but all of the other audio (speech, sound effects, etc.) seem to play fine throughout the entire game.