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Thanks for your post.
Does the error always happen at the same point with whatever backup file is used? If the backup is situated on a network share, my initial guess would be that there was some kind of network glitch that caused the connection to drop. there isn't anything in the tool to recover from a network outage, so this might be a possibility.
Would you be able to try using SQL Virtual Restore to mount the backup file?
<http://www.red-gate.com/products/dba/sql-virtual-restore/>
This will probably give you better results, as it will allow you to compare the backup file as a live database, rather than the slightly more limited comparison you can do directly through SQL Data Compare backup reader.
I hope this helps.
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The strange thing is, when I open the BAK file, it immediately tells me the info in the start-screen. It shows me that the file contains a full backup, data and the correct database. But then, when I start comparing, it fails.
Can anybody tell me what I have to check to make SQL backup files work with SQL data compare PRO? Maybe specific security settings?