I've just gone through some of this with NetApp support.
Are the primary paths that are not showing up in DFM non-qtrees? If they are, the snapvault path needs to be /vol/volname/- in order for DFM to recognize them.
It's kind of difficult to describe here, but you can correct this on the secondary by running:
snapvault modify -S <pri_filer>:/vol/volname/- /vol/volname/qtree
then
snapvault start -r /vol/volname/qtree
You'll then need to remove the old snapvault relationships on the primary (the ones without the /-)
snapvault release /vol/volname <sec_filer>:/vol/volname/qtree
Hope this helps some.
Richard