"Nominal Pan" on the new Yamaha mixers refers to the level relationship between fully panned and center panned material.
The nominal pan setting would give you unity gain ("0") when the fader is at 0 and the pan is fully left or right, and, I believe, -3 when the pan is set to center.
The other setting gives you unity at the center and +3 at full pan....this setting is for folks who want to bring a fader up to 0 to achieve unity, which is a common need in the broadcast environment.
There is a whole other set of concerns and arguments about how far down the center dip should go (-3, -4.5 or -6), but that is too much to get into here, and I don't believe this is software-selectable on the Yamaha mixers.
As far as surround, you should check your preferences page to see how this all translates. I have not done surround on my 01V96, but my first DM2000 did not translate the panning setup properly to the surround buss panning. My second one did, but I don't remember if it required a property to be checked in the preferences menu....this had not been an issue with the 02R. If your 01V96 is Version 2 or higher, you should be able to set up the pan properly for the busses to reflect the way you want to mix.....The "nominal center" panning can run you out of headroom more easily than the "nominal pan" setting, since everything goes up by 3db.