I do have the Navigator setup to display me all the heading levels but the Heading3 is missing from it, still Heading1,2 and 4 are visible.
When I compute the index, I do see all of them.
What i is the cause for this?
Note: LibreOffice is 3.5.4.2 running on OS X.
Can’t reproduce this. Please add a screenshot of your navigator window or attach an example document.
It is possible that this is due to a custom heading style being in use. Navigator does not appear to show custom heading styles. I have also seen this for the standard heading styles, although on rarer occasion. I do not not put a lot of stock in Navigator and thus use it infrequently, however I would be interested to know why this behaviour does occur.
@ tohuwawohu - does the upload facility work yet? Not working here under Ubuntu x86_64 / Firefox 13.0.1. If I could attach a screenshot / sample doc I would.
As oweng mentions,
Navigator does not appear to show custom heading styles
I’m not sure if this is a bug or just a feature we should add…
Well scratch that – @CyanCG says that this should work! (see comment below)
Actually, by adding the custom styles to the document’s “Outline numbering” in Tools > Outline numbering, the custom styles will be displayed in the Navigator. I have tested it at least once. So there really is no bug or missing feature, just check the style properties as always 
For an example of how this is done, one can download the ODT file of the ODF 1.2 spec, which is a prime example for the implementation of various features.