PAUSE/RESUME is definitely problematic for a number of reasons besides this. The much better way to stop and restart a script now is with THROW CONTEXT. It lets you assign a variable name that can then be used to restart the script exactly where it left off. See http://chemapps.stolaf.edu/jmol/docs/#throw. I would encourage you to switch to that if possible. It is really pretty amazing. You can check and change variables and then restart anytime, regardless of how many other scripts have been run or are halted with other THROW commands.
Bob
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