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I went through and updated all of the CSS files just before release Zen 7.x-3.0. But I didn't realize the simplification I made to the CSS caused the bullets to mistakenly re-appear for the Main menu and Secondary menu links.
The easiest way to fix this is to add a "inline" class to both of those ULs. That's what core's page.tpl.php does, but Zen's page.tpl.php currently does not.