If the layer is not hidden and it's not displayed on preview, then yes, chances are that it is a pop-up layer. To make it a static layer, you must remove all the references you have to this pop-up layer. If there is no object that is linked to the pop-up layer, then the layer is static. As soon as you add a link to this layer to any object, it automatically becomes a pop-up.
But if you want to know for sure why the layer is not visible on export in the particular design, you'd better attach your .web file and we shall tell what's wrong with it.