I couldn’t pinpoint your problem, but it probably has to do with the fact that Unity internally uses power of two texture sizes for everything. What I’d suggest is, for instance, to never use 1024 x 768 as the ‘desired’ size in syphon, and instead use 1024 x 1024. it will scale to your surface, then your can resize the aspect ratio of surfaces appropriately. This may be turn out to be an issue with projectors, which do not necessarily conform to surface UV’s in the same way that regular textures do.
From Aras : http://forum.unity3d.com/threads/18607-POT-and-NPOT-textures-problem
“And do not worry about hardware support; we do store textures at NPOT size (to save space), but at load time we create a texture that is next power of two, and pad that texture with dummy pixels (and if original NPOT texture is DXT compressed, we blit the DXT compressed blocks and fill the rest with dummy DXT blocks – so the resulting texture is still DXT compressed). And then we do some magic so that GUI that uses that texture is still always referencing the correct portion of that “padded up” texture.”