Hi. So first off, I have audio, but its choppy. I tested this on my Linux PC and on the Steam Deck too. Both have different configurations. The very first short logo in the beginning saying Nintendo and the ball coming in already has this issue. Then later when starting a new game, the animated intro sequence with spoken dialogue has this issue too.
It is probably an issue with some video codec. It plays at lower “FPS” around 34 or so. After the video sequence ends, the game jumps back to normal. I have versions of the game here “Pokemon Puzzle League (USA)” and “Pokemon Puzzle League (USA) (Wii Virtual Console)”. Interestingly the Virtual Console version on the Wii does not have both video intro sequences. Maybe Nintendo had some trouble to emulate and removed them? Just some speculation.
As I have the Steam Deck, and some choppy sound, you can try my emulator settings. I have RetroArch installed through the Steam store, version 1.21.0 right now. My RetroArch Settings > Audio > Output > Audio is set to “pulse”. Running the Mupen64Plus-Next core, the Core Options are RDP Plugin set to GLideN64, generally settings tried to be close as original hardware, CPU Core set to Dynarec, RSP Plugin to HLE.