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I have several Samba mounts on an Ubuntu server. When I ssh into that box remotely (instead of working directly on the box), I cannot see the mounted file systems (ie, if I ls there are no results).

Is this normal, have my mounts failed to load in my absense, or is something else at play?

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How are your samba shares being mounted? Do you use /etc/fstab like:

//servername/sharename /mountdirectory smbfs username=windowsuserename,password=windowspassword 0 0

or do you mount them through file manager (nautilus or some similiar), and use Gnome Virtual File System (gvfs)?
If your mounts are permanents, through fstab, you should see them always, unless you have your ssh sessions, chrooted (in a safe sandbox).
To mount your samba share/resource manually you could use:

mount -t smbfs //servername/sharename /mountdirectory -o  username=mywindowsusername,password=mywindowspassword

Can you post the output for the mount command on both scenarios, local session and ssh?

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