Without knowing machine construction and control schematic
i would say....
If the symptoms are as described
ie. when you manually keep run command valid
machine is carried out the work sequence from beginning to end.
but the auto sequence is interrupted
I would assume that some limit switch , relay contact or coil does not work
because the sequence of functions does not remain connected on ,
until the normal end of sequence.
( or the sequence stop contact is allways on , depends on : how the circuit is designed )