Setting the item margin in the option set doesn't set a margin on the slide items.
This is apparently the way the FlexSlider library works, by design. Margins are supposed to be set in CSS, and the "itemMargin" property merely informs FlexSlider of the margins so it can calculate carousel movement and sizing properly.
Perhaps we could have the Drupal module to generate the appropriate CSS style if an itemMargin is given in the optionset, but that'd be a new feature. In the mean time, I've committed an update to the description on the admin page.
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