Would you please try this:
Start up an affected version (i.e. latest dev build), go into Options > Hotkey Settings. Click "Clear". Click "Ok". Start the game.
Let us know if this works for you.
The reason why this occurred is that the Key Shortcut and the Hotkey were assigned to the same keys by Dolphin. Dolphin responds to both the Key Shortcut and the Hotkey resulting in the double up. This has now been changed, but the config file that came from the old version might still be hanging around (if those old versions were used at a point in time).
Start up an affected version (i.e. latest dev build), go into Options > Hotkey Settings. Click "Clear". Click "Ok". Start the game.
Let us know if this works for you.
The reason why this occurred is that the Key Shortcut and the Hotkey were assigned to the same keys by Dolphin. Dolphin responds to both the Key Shortcut and the Hotkey resulting in the double up. This has now been changed, but the config file that came from the old version might still be hanging around (if those old versions were used at a point in time).