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I'm not sure if there is something wrong with your system because I don't have the details on how you are trying to back it up. You can take online backups of Exchange 5.5 using both the built-in Windows NT Backup utility or by using a third-party utility.
First, take a look at the Disaster Recovery for Exchange 5.5 white paper at http://www.microsoft.com/exchange/techinfo/administration/55/BackupRestore.asp. In addition, see the following documents:
If you are using a third-party tool to take the backup, consult that tool's documentation for instructions on how to back up Exchange online.
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