Hey Lemo, 
   If you want to reverse the Y axis in relation to the Y button, here is a place in the code you can change it.
Make a new gloabal int var called: 
int JoggDirValue;
//thien in the ShuttleWin.cpp find the below 
case( 810 ): 
               if(LockWheel) 
               {
                  SetMachError( " Wheel Locked. Unlock first. ");
                  break;
               }
               Jogging = true;
               ////////////////////////////// what I added //////////
                    if (CurrentAxis == 1) 
                    {JoggDirValue = 1;} //reverses the direction of the Y
                    else
                    {JoggDirValue = 0;}
                    //////////////////////////////////////////////////////
               Engine->Axis[ CurrentAxis ].MaxVelocity = MainPlanner->Vels[ CurrentAxis ]; 
               Engine->Axis[ CurrentAxis ].Acceleration = MainPlanner->Accs[  CurrentAxis ];
               Engine->Axis[ CurrentAxis ].MasterVelocity = MainPlanner->Vels[  CurrentAxis ];
               Engine->Axis[ CurrentAxis ].Dec = false;
               Engine->Axis[ CurrentAxis ].Jogging = true;
               Engine->Axis[ CurrentAxis ].JoggDir = JoggDirValue; //normally 0, for all other axis but Y then = 1
               Code("DOJOG");
               break;
      case( 811 ): 
               if(LockWheel) 
               {
                  SetMachError( " Wheel Locked. Unlock first. ");
                  break;
               }
               Jogging = true;
               ////////////////////////////// what I added //////////
                    if (CurrentAxis == 1) 
                    {JoggDirValue = 0;}  //reverses the direction of the Y
                    else
                    {JoggDirValue = 1;}
                    //////////////////////////////////////////////////////
               Engine->Axis[ CurrentAxis ].MaxVelocity = MainPlanner->Vels[ CurrentAxis ]; 
               Engine->Axis[ CurrentAxis ].Acceleration = MainPlanner->Accs[  CurrentAxis ];
               Engine->Axis[ CurrentAxis ].MasterVelocity = MainPlanner->Vels[  CurrentAxis ];
               Engine->Axis[ CurrentAxis ].Dec = false;
               Engine->Axis[ CurrentAxis ].Jogging = true;
               Engine->Axis[ CurrentAxis ].JoggDir = JoggDirValue; //normally 1, for all other axis but Y then = 0
               Code("DOJOG");
               break;
//scott