Why do some elements disappear in HTML or XLS output?

The most probable cause of this is the fact that these elements overlap with some other elements. The XLSX, XLS, DOCX and the ODS exporters are so-called grid exporters. They arrange the content of a document page in a grid using a positioning algorithm. In each cell of the resulting grid we can put only one element, so the elements that are placed behind some other elements will be ignored when exporting to these formats and will not appear. The missing elements could overlap with only one or few pixels, but that is enough for then to be removed from the grid.

To avoid this effect, you should follow the recommendations in this other FAQ about  making grid exporter friendly reports.