I agree to @nascif_jmp , as a platform switch Always is a Chance to have Trouble.
Why also not Performing the whole Job in jmp?
By the way, the Shell call for a jmp Job works as simple as follows:
Path2JMP\jmp.exe script.jsl
and if the script starts with "//!", it is excecuted on Opening,
and you can quit at the end.
See Scripting guide --> getting started (or search for //!)
//!
Names Default To Here( 1 );
// here Comes the JMP Job ...
Quit();
Georg