I knew that the plugin had been changed from earlier versions so that you could use the arrow key to jog when in motor tuning and just presumed this would take consideration of changes in settings. However I have just tried it and it seems to be that you have to come out of motor tuning before you can try the new settings, that sort of defeats the functionality of being able to jog when in tuning, I will see what Greg says about it.
As for your Y not being correct, it could be many things, have you had it running on the parallel port? If not then you may have to swap around axis to see if you can shift the problem over as it could be anything from SS to motor tuning to motor to breakout etc. If you have a scope it would be fairly easy to see where the problem lies.
Hood