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My guess would be some kind of variable is getting hosed up. When you run a script in PyScripter and then run it again, PyScripter resets Python between the two runs. However, PSSE runs the script the second time from where the first run left off, so all the variables are still in scope.

To test this, run your script, then run the commands below, then run your script again. If it works fine, you know that its because of how your script is leaving the variables when it exits.

import sys
this = sys.modules[__name__]
for n in dir():
    if n[0]!='_': delattr(this, n)