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Hmm, I thought the Cokin Z-Pro came configured with all three slots on the outside -- one thick one and two thin ones -- at least I'm sure that's how mine came. When that's the case, I think your report of vignetting sounds about right. If it really is set up with only two thin slots on the outboard side of the holder, then something doesn't add up. That is currently how I have mine configured, and (with a 5DII and 17-40) it does not vignette when the holder is square with the camera frame. When the holder is rotated to 45 degrees, I get vignetting in the corners that is gone by about 19 mm.
You have probably realized that it isn't the holder frame itself that hits the corners, but rather the stack of filter holder slots. The more slots you have stacked, the greater the likelihood of vignetting. The actual geometry of this depends on details of the lens design and doesn't correlate directly to focal length alone. I've found the 17-40 to be slightly more prone to this than was my 10-22 on a crop, at equivalent focal lengths.
There are two things you can do: take off filter holder slots until they no longer vignette (or the degree of vignetting at wider focal lengths is something you can live with); or mount the adapter ring in the first (thin) slot on the OUTSIDE of the holder frame, so that everything is set back by a distance equal to the thickness of the frame. The latter approach is fiddly and a pain, but some people use it successfully (after they get used to it).