It seems to me that your phono board is not powered up as it should be.
The really low volume is like you feeding your phono signal directly into a high level input, without the amplification of a phono preamp circuit.
Of course I'm sure you have your phono signal plugged into the correct inputs on the back of your Yamaha, but an unpowered phono preamp circuit would just be passing your signal directly to your high level preamp at a low level that would require a high setting on the volume control.
Maybe a service check is warranted.
The really low volume is like you feeding your phono signal directly into a high level input, without the amplification of a phono preamp circuit.
Of course I'm sure you have your phono signal plugged into the correct inputs on the back of your Yamaha, but an unpowered phono preamp circuit would just be passing your signal directly to your high level preamp at a low level that would require a high setting on the volume control.
Maybe a service check is warranted.