gmshToFoam creating bad mesh from self-written .msh file
 

So, I wrote a MatLab code that generates a .msh file from a list of points. It worked perfectly until I tried to add a refined area to the grid. The boundary of the refined region is behaving as if it is a wall when there should be no boundary at all (see screen shots). There are no apparent differences in the .msh files however, running gmshToFoam generates errors and allocates cells to a defaultFaces patch. It's a simpleFoam simulation and I realize that the grid is far too coarse but that shouldn't have anything to do with the current problem.

Any ideas why this might be happening? I'm sure it has something to do with the errors that gmshToFoam reports but I'm not sure exactly what they mean.

Here is a Google Drive that includes the case files and the .msh file (matlabMesh.msh).

https://drive.google.com/a/fau.edu/#folders /0B4WyR3TZFuZkYnFEdG5STkdCMjA

and here is an imgur gallery with some relevant screenshots.

http://imgur.com/a/FmtUn