Hello
If you turn the spindle manually, then the reference mark is run over so it’s marked as “referenced”.. That also happens when the spindle starts-up.
Try a tool change and write the spindle command in a separate row.
T1 D1
S500 M3
or
T1 D1
S1=500 M1=3
If that doesn’t work then you should search for any hardware errors with the help of the service.