It sounds like there might be a misconfiguration in your firmware settings. Here are a few potential issues and solutions:
Double-check the steps per millimeter settings for the X, Y, and Z axes in your firmware's configuration file. Make sure the values are set correctly for your specific hardware. You can use online calculators or run calibration tests to determine the correct values.
Verify that the microstepping settings for the TMC2209 drivers are properly defined in the firmware. The default microstepping value is usually 16, but you should confirm it matches your hardware setup.
Check if the motor drivetrain (belts, pulleys, lead screws, etc.) is properly tensioned and not slipping. Loose or misaligned components can cause incorrect movement and affect the accuracy of your prints.
Ensure that your printer's physical steps per millimeter jumpers (if any) are correctly set. Consult the documentation or manufacturer's guidelines for your specific printer model.
I've got it in my head that because I am using Z1 and Z2 on the board as it has 2 channels that I've missed something due to X and Y working perfectly.
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