Why does NetWorker perform a bootstrap backup after every group runs?

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If the server is not listed in any active groups, the server's bootstrap (containing the media index and the server's client index) will back up every time every group runs. This is a safeguard. To prevent this, put the server in an active group. There is a "feature" in Networker 6.0.1 that even for skipped savegroups, it will still write a bootstrap into the server's tape drive.