You have the settings set incorrectly. The issues you list are hard to follow, but most, if not all are addressed by the firmware settings and then telling LightBurn what settings you have. LightBurn talks to the control board. The control board has settings in firmware. If these settings are not set properly, you will see many of the issues you are observing.
What firmware, including the version number, are you using to drive this Neje? Have you recently updated this firmware?