The layers order is important as described in the help. However it can not influence layers visibility.
If some of your visible layers do not show on the exported page, then they are a pop-up layers.
Any not rollover layer may become a pop-up layer if you have any object on the page that is linked to this layer as a pop-up. There are two ways of linking object to the pop-up layer (and thus letting program know that this layer is a pop-up):
1. Web properties dialog / Link tab / "Pop-up layer" field.
2. Web properties dialog / Mouse-over tab / "Show popup layer" field.