Hi kostas

Um - that is a bit strange, if it worked with a red cross there.
The Y Step pulse width may be not quite enough for proper operation in this mode. This is a known problem as well, and Mach has a setting for it.

Try this with the Y axis set to a green tick for Step Active Low:
Config, Motor Tuning, click on Y axis, look at 'Step Pulse 1-5 uS'. This is probably set to 0. Change it to 2 and then click on Save Settings.
Now click on X axis and make sure that Step Pulse is set to 2. If not, repeat the above.
Click on OK, then go back to Config and click on 'Save Settings'.
Now try.
Note that you MUST click on 'Save Settings in two places.

Cheers
Roger