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That suggests that there's something unusual about your backup file that means our backup file parser can't find sysindexes. I don't suppose you can send us that backup file (to michelle.taylor@red-gate.com) so we can have a look at it? Any further information about it (how many backup sets are in the file, what kind of backup / version of SQL Server are they, how big is your database) might be useful in tracking down the problem.
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I received an email from support on Sept 15 telling me to download and install ftp://support.red-gate.com//Patches/SQL_Data Compare/SQL Data Compare_7.0.0.560.zip. This fixed the problem. The call reference number was F0015387.
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I was able to pick the set of tables that I wanted to compare just fine.
When I clicked Compare Now, it died on the Comparing databases step with the error 'SQLite error no such table: sysindexes.
The main reason I upgraded to the Pro version was to be able to compare backup files with a live db.