The button-combo method of access the emulator menu, such as Start and X, + and -, 1 and 2, etc. results in an issue where both of the actual inputs are still sent to the game itself. This issue however is present even in Wii64 and Not64, so it's extremely possible that it's simply inherent to the front-end.
This issue most greatly impacts the GameCube, wiimote+nunchuck, as well as wiimote by itself controller configurations since those three controller configurations do not have the option to access the emulator menu with only a single button in the way that something like the classic controller does (whereby you can workaround the issue by setting the emulator menu button to "Home" and then simply not mapping any of the dualshock buttons to "Home")
The button-combo method of access the emulator menu, such as Start and X, + and -, 1 and 2, etc. results in an issue where both of the actual inputs are still sent to the game itself. This issue however is present even in Wii64 and Not64, so it's extremely possible that it's simply inherent to the front-end.
This issue most greatly impacts the GameCube, wiimote+nunchuck, as well as wiimote by itself controller configurations since those three controller configurations do not have the option to access the emulator menu with only a single button in the way that something like the classic controller does (whereby you can workaround the issue by setting the emulator menu button to "Home" and then simply not mapping any of the dualshock buttons to "Home")