I personally haven't encountered this issue, so forgive me, if I can't help you with this very problem.
However, may I suggest NOT to use inline scripts at all? What I like to do, is to keep all my scripts in jiraHome/scripts directory and simply specify a path to a relevant file in my scripted fields, listeners, postfunctions, etc. Furthermore, using a version control system (like Git or Subversion) to store all your code will help you easily restore it, in case something goes wrong.
Hope this helps.
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