How are your samba shares being mounted? Do you use
//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?