One of the errors I encountered with the Red Gate Backup Pro tools discussed extensively this month, was in running the DBCC CHECKDB command on a temporarily restored backup.  It gave errors about the consistency which did not appear in the actual master database.  The following are some interesting blog articles in response to this issue:

1. Response from Red Gate.
2. Response from Paul Randal and Kimberly Tripp on SQL Server Pro magazine.

Basically you will need to do the master database separately.  I run an integrity check weekly against the system databases.  It is a good idea to follow the recommendations from Red Gate listed in the link above.  Enjoy!