The charges for the diagonal of the charge Burden Matrix in BCUTDescriptor.java are not sent to BurdenMatrix.evalMatrix. The charges are calculated in calculate() but they are not used. Instead the diagonal is set to a vector of ones. CDK 1.3.12
Patch provided https://sourceforge.net/tracker/?func=detail&aid=3349039&group_id=20024&atid=320024
Patch provided https://sourceforge.net/tracker/?func=detail&aid=3349039&group_id=20024&atid=320024