Not to be joking, but are you sure that you are using the phones jack and not the line jack?
Did you try the line output jack to see if that is affected by the phones volume control? I didn't look to see if those jacks are board mount or discretely wired. If they are discretely wired, it's possible that line and phone jacks were reversed during assembly.
In my case, the headphone jack and volume control worked as expected.
If you can't solve this, write SD through the support page. They have been really responsive for me.