Originally posted by R@nSiD
DO a cleanup operation on the geometry. If you are not getting to delete some of the veryts it usually indicates a problem with the edgeds connectiong.
I suggest going in and removeing the faces on either sdie of the geometry, but it does sound like you have kinda opened a can of worms.
Eye that might sort it.
You might also have a normal in the wrong direction so id give it a go checking the normals.
As Chris said it can be a pain to get it sorted.
Sometimes the script editor makes its own scripts that help you out, you might need to open the script editor to see the full text.
"No pressure, no diamonds" Thomas Carlyle