Hi Jennine,
The ROI should be in pretty much the same are on both the original and the standard mesh surface. If you say that the standard-mesh --> volume ROI was correct then the problem is in the volume ROI --> original mesh step.
One way to help you find the problem would be to load the original mesh in suma and the volume ROI in AFNI and see how the surface intersects with the volume ROI. If there is poor alignment then you might be using the wrong surface volume.
I can't help much more at the moment because I am busy getting ready for a talk. Let us know how it goes.
cheers.
-ziad