jonnyk,
The volume control on the sub controls the amount of applification done by the sub on the input signal. The level of that input signal is controlled by your Yamaha. So, yes, the volume of the sub will be affected by how you adjust the volume on your receiver...as it should be. It's possible that the level of that sub signal is set very low on the Yamaha: could be that your sub level is set low (somewhere in the negative dB range), or it could be that you have your speakers set up so that little or no bass is actually being sent to your sub. Check your speaker settings. I'd be interested in knowing if you've solved your problem.
Adam