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If elements in your project aren't showing up or links aren't working when you publish your website, they are most likely being covered by a background layer or accidentally placed on the "MouseOver" layer.
Check the "Page and Layer Gallery" and either delete the layer covering the elements or move the elements you want to be visible all the time to one of the "MouseOff" layers.
Elements such as images and text must always be placed on the "MouseOff" layer.