I did a database comparison between a plain site installed with the wizard, and one created manually using kernel_schema.sql and cleandata.sql and the main difference is...
Locale. cleandata.sql loads content for the en-GB locale, but my siteaccess was setup for en-CA content.
In the "Manual configuration of eZ publish" document at the bottom is a section called "Translation settings in database". This section is mandatory if you use a different locale.
You MUST run these commands (using your locale) before being able to load your user or admin sites.
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