I believe understand the problem after speaking with another colleague.
The issue here is the JMP user interface will not allow one to save a table, with Auto Open selected, while an invalid Link Reference path exists. The JMP UI will save the table but will set the Auto Open option. So the table can be opened or recovered.
In JSL however, it is permitted. The table is saved with Auto Open and an invalid Link Reference. This prevents JMP from opening the table. The JMP UI has some sort of safety check in place that is not built into JSL.
I've reported this issue so it can be addressed in a future release.
Best!