Tracking does not need cLLD on as it moves based on the define dimensions of the labware well and how much volume is dispensed. So mathematically calculation of the height to move. So the Labware well needs to be correctly defined.
Sounds like you have modified the microscript so without knowing what you have done it is difficult to correct this. I would duplicate a fresh LC and see if the movement behave what way you need it to first and then see if you can spot the difference in the microscript.
The alternative is to keep cLLD with tracking on but have the LC error handling to ignore and continue if the well is empty. This is an FCA command you can put at the start of your script to stop getting error handling box flags.