Thanks for you comment, the first loop runs but the second loop that is making charts associtated with a different data tabe than the first loop is not running. But then after the scritp is done I highlight just that second loop and run only that part and it works fine. It will update the window with the correct analysis from that second table. It seems that I can't add analysis to the window from different tables without the scritp stopping and then I run just that second loop.
Did you confirm that there are no error messages in the log? Your first loop iterates over 6 columns - do all 6 reports appear in the window? I'm not sure how you are confirming that the second loop "is not running". It might help to add Print() statements or use the JSL debugger to see exactly where the script stops, if the log messages do not clarify this.
I modified your script to run with sample data (one Y each) and using multiple tables is not a problem in JMP 14: