Ok - we'll need to narrow down where the build process is being handled differently between the grid node and the VS addin.
In both cases, the build will be run within a specialised workspace built by NCrunch. What we'll need to do is obtain two workspaces - one for the NCrunch VSAddin build, one for the grid node build. We then compare the workspaces and their project files in an effort to figure out why the build will work in one but not in the other.
Finding a workspace for an NCrunch VSAddin build is simple. Just switch off all the remote grid nodes, then let NCrunch build your project. Right click on the project in the Tests Window and go to Advanced->Browse to workspace. Perhaps consider making a copy of this workspace so you can refer back to it if NCrunch later removes it (which it does routinely). As you've mentioned, this is the workspace that works correctly.
Finding a workspace for the grid node is a little more difficult. If you run the Grid Node config tool, you'll find an option to set the 'Workspace base path network share'. Set this value to be the same as the workspace base path. Once you've done this, go into the NCrunch VSAddin and disable all processing except for the grid node you've just configured. Let the grid node build the project. Find the failed project build in the Tests Window, then right click on it, go to Advanced->Browse to workspace. This should be the workspace that is failing. Make a copy of it.
Try comparing the two workspaces, with close attention to the project file. Do you notice any differences that could be related to the build problem you're experiencing?