Ok, you have it working from the test software (which I am not familar with), so we know the board is working.
You idicate the you found the pin settings "somewhere". WHERE? If you can figure out what pin settings the test software used, you can set up Turbocnc to follow the SAME settings.
It sounds like "somewhere" may not be the settings the test software is using OR you have the sense direction incorrect. But first, you must find out what the actual settings are that ARE working.
Don't dispair, it will fall into place quickly.