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). http://en.wikipedia.org/wiki/Chrooted
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?