This is not a file type specific bug but seems to occur with all the files conkeror does not
automatically open internally or via mimeTypes.rdf. By the way, the latter also provides a work-around:
If you are willing to let conkeror run the same command on all, say, PDF-files, you might want to edit
mimeTypes.rdf accordingly (e.g. with the help of the preferences dialogue in firefox, under "Applications").