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If there's a difference in the Filestream definition that's causing it to be listed then I'd expect that to show in the difference pane, assuming the text for that is displayed.
Do you have extended properties on the table? If so, can you try ignoring these in the options and see if it stops it showing up; as I've seen occasions previously where invisible whitespace differences in your extended properties text cause an object to be flagged as different, but you cannot see this in the diff pane. -
I already have Ignore Whitespace enabled. After enabling Ignore Extended Properties, I get the same response.
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Is it possible for you to script out the two tables so I can test it out here? Feel free to send them to support@red-gate.com referencing this forum topic and I can get a ticket opened up to check it's nothing odd.
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Just for grins, I have executed the synchronization script but still get the same compare results.
The only thing 'special' about this table is that it contains a FILESTREAM column. ???