Set Dolphin to use real wiimotes and set the dolphinbar to mode 4. Then enable continuous scanning and disable speaker data.
And if that still doesn't work, reconnect manually by pressing alt f5. Which is required for multi .dol games, like for example Metroid Prime Trilogy anyways.
And if that still doesn't work, reconnect manually by pressing alt f5. Which is required for multi .dol games, like for example Metroid Prime Trilogy anyways.