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You either have the Default theme set as your main theme or have your categories set to the Default theme.
Admin > System > Configuration >Design > Themes Dropdown > Make sure your themes name is in the “Default” field
You can also specify which category leads to what theme by going to:
Admin > Catalog > Manage Categories > Choose the category to change > From that categories top menu (should be 4); choose “Custom Design”, and pick your theme for that category.
Hope this helps