I believe there is a bug in the code that creates subtasks. Looking at your source, you have a parameter called "SKIP_EPIC_LINKS". But it looks like that does not get passed in the call from CreateSubTask to AbstractCloneIssue.
Hence my auto-created subtasks have Epic Link values. The Jira GUI explicitly stops the user from editing that field (only on subtasks) because it knows it should not be there!