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I am pushing another commit which tries harder to clean out existing numeric rename targets. Will post a download link when available. This is looking like some weirdness in how Windows handles symbolic links, which varies not only according to Windows version but also depending on filesystem and system configuration. Unfortunately Jenkins makes heavy use of the filesystem to store data, and lots of things behave unpredictably on Windows servers.
You are encouraged to use Java 7 (or 8) rather than Java 6, as you will get better diagnostics: the file APIs available in Java 6- are poor.
You should also go to /log/ (Log Manager) and create a custom log recording jenkins.model.RunIdMigrator at FINE. After the migrator runs at startup, logs are available in that URL. If they are truncated (only latest messages shown), you can install the Support Core plugin to capture fuller logs.