You do not need any M563 commands in your slicer start gcode, only in config.g. Use a T0 command in the slicer start gcode.
One possible source of confusion is that the M0 command you use at the end of a print deselects all tools. If you have T0 at the end of config.g but not in your slicer start gcode, then your first print attempt will succeed but subsequent ones may fail.
One possible source of confusion is that the M0 command you use at the end of a print deselects all tools. If you have T0 at the end of config.g but not in your slicer start gcode, then your first print attempt will succeed but subsequent ones may fail.