If you are generating output using "XMetaL Enhanced PDF via RenderX XEP" this is by design (ie: I believe the people that wrote the XSLT/XSL-FO thought it was a good idea).
In order to give you some pointers on where you might alter the XSLT to get what you want I think it would be best to see your files. Bookmaps are quite flexible (chapter can appear inside various other elements) and any XSLT alterations might need to be made specific to your type of bookmap.
However, if things are outputting as you like for
<topicref> have you tried creating this type of structure?
<chapter>
<topicref format="dita" href="mytopic.xml" navtitle="my navigation title" scope="local" type="topic"></topicref>
</chapter>
Can I assume you have something like this?
<chapter format="dita" href="mytopic.xml" navtitle="my navigation title" scope="local" type="topic"></chapter>