Hi, Thkoutsidthebox
If you hit the Tab key it will allow you to un-select the Shuttle Mode, Hit the Tab key again the window will close.
As far as your Y axis direction, Hard to say what caused it, Check your Config, Ports & Pins, Outputs as Jim stated, But Thy should all be in the same for Dir and Step, Ether Active Low or High, "Checked or X".
If an axis is backwards, Change it in Config, Homes & Limits Page, Use the Reverse Box, Ether "Checked or X", Some stepper controls don't work or preform poorly if the Active Low or High are set wrong/mismatched.
Hope this Helps, Chip