sql data compare 8.1 generated sync script problem

SQL Data compare 8.1 can sync a series of tables from two different DBs great, but when I try to run the script it generates, I get a

Violation of PRIMARY KEY constraint 'PK_XXX'. Cannot insert duplicate key in object 'security.XXX'.

Even though there is no data anywhere in that table.

Has anyone encountered this? Where the SQL Data Compare itself can sync tables, but the script it generates is busted.

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