Command line scriptfile, no keys or indexes for tables

On the command line, when comparing two script folders, the script that it generates does not contain any keys or indexes for tables. Am I doing something wrong? Here is the command line I am using:

SQLCompare /scripts1:C:\Source-Latest\RedGateScripts /scripts2:C:\Source-Previous\RedGateScripts /scriptfile:C:\Output\Upgrade.sql

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