In SQL Data Compare 5, after you have done a synch where not all of the rows were synched, the check box at the top still shows as partially checked, rather than returning to it's unchecked state. From there, if you check one of the items for inclusion at the bottom, the check turns off, and removing the check, so that none of the rows are checked returns the master check to the partial state. Checking the master check box clears up the problem.
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