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If you have tables with primary keys in the source database, they should be copied to the target database along with the table. Check that you don't have the 'Ignore Indexes' option selected - primary keys are indexes and will be ignored by this option.
Other than that, I'm not sure what's causing your problems - if you could give me some more details about the tables in question (ideally by sending a snapshot or backup to michelle.taylor@red-gate.com, but I understand not everyone can do this) and about exactly what options you are using in your project I might be able to work out what the problem wasd.
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Any ideas of how I can get it to create the primary keys?
v 6.2.0.271