i encountered the same problem. I installed unison-gtk via Synaptic.
Local syncing works, but remote syncing fails, because unison-gtk on
"source" machine wants to call unison on "target", not unison-gtk.
Manually installing unison with apt-get helps, of course, but it takes a
while to figure that out.

-- 
unison-gtk should depend on unison
https://launchpad.net/bugs/49468

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