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First a description of my environment:

Toshiba laptop - dual boot Windows 7 and Debian/Jessie
I "had" two mount points:
1) /media/windows (local partition for sharing files with Windows).
2) /media/shares (NFS mount to my Debian/Wheezy server)

When I checked the box for "Show connected volumes on the desktop" in "Desktop Settings", both mounts would be displayed.
OK so far but I get messages lke this in the syslog & messages files:

org.gtk.Private.UDisks2VolumeMonitor[1059]: index_parse.c:191: indx_parse(): error opening /media/windows/BDMV/index.bdmv


Apparently the UDisk2 Volume Monitor thinks everything in /media is a Blu-Ray disk.
At least that is what googling BDMV implied..

So I moved the mount point to /net/windows and /net/shares and no more messages.
Now however, the mounts don't show up on the desktop.

Does anybody know how to work around this issue?

I think you should report the issue to Udisks2 instead as it clearly seems as a bug for me.
Or just ignore that syslog message.
Alternatively you can simply add links to your /net/shares and /net/windows on your desktop by dragging their icons from the file manager window with both Shift and Ctrl keys pressed (to force link drop).

are those volumes in your /etc/fstab?
you might want to try the "comment=x-gvfs-show" setting, e.g.: (just an example, as i don't have an actual NTFS drive to mount).
this will make mounted partitions show up in my filemanagers sidebar.
hope this helps.