[Freesurfer] wmparc/white matter problems?

Hello,

We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.

Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?

Any help is much appreciated!

-Ryan