well the settings are correct
I have a bad feeling the prolem is in the Tyrol not the software 
Q1
ok x-axis works correctly - jogs both ways and homes correctly?
let's focus on the y axis first
what happens when you try to jog in each direction?
does it move at all?
does it move 1cm every time?
does it work both ways?
what happens to y when you hit home (once)
finally - (dangerous stuff now)
in CNCdriver, the big window top left
you can type commands in there - scary
try this, it will report where the Arduino thinks X, Y and Z are as well as the state of the limit switches
first jog the x and y so they are away from home
hit home once
then clear the big window and type
M114
hit the run button and tell me what you get in the middle window
(you can resize them if it helps)
cheers
Mike