If you actually browse to your drawcall you can get a lot more detailed information about the vertex buffer, by doing what you are currently doing you will only see the input buffer not the transformed one after the VS has run. And it can well be that your input buffer is correct but the output of the vertex shader isn't, I am assuming you are using a vertex shader here. Even if you are not using a vertex shader looking at when the drawcall is submitted will give you an idea of whether your transforms are correctly transforming your vertices in the buffer. Also it will tell you whether they are within the viewport or not which can also affect what you see on screen.
So just hit the plus on that frame you captured and look through the drawcalls till you find something that is rendering with that vertex buffer. By the way if you extend the list of a frame it will show you which commands your are actually sending to the D3D runtime from your application. Hit F1 in pix and look for this subject in the help file "View Buffer Data" checking out subject "View Mesh Data" is also a good idea. You can find this in the DirectX Software Development Kit help file under:
-DirectX Software Development Kit -Tools -DirectX Performance Tools -PIX -Tutorials and Samples