Okay, so you calibrated manually with the aid of an SPL meter. If you did it correctly you should now be getting the same sub level which you had before. It's a little surprising that the changed volume control on the new amp would require that much increase in the Yamaha sub output, but as long as it's now properly calibrated to match the speakers there's no cause for concern.
It surprised me also.
I had to bump the decibel level and increase the volume knob level.
I could have bumped the decibels even higher on Yamaha and left the volume knob at 9 O'clock but I remember reading somewhere that you should never go higher than +3db on sub speaker level.
