Prepayment penalties appear to be doing their job, slowing repayment rates on subprime mortgages. But a recent report by a Wall Street investment house suggests that penalties alone don’t tell the whole story. Data from the San Francisco-based Mortgage Information Corp. suggests that prepayment penalties, generally a percentage of the loan amount charged to borrowers who repay their loan within a three- to five-year window after origination, can slow refinancing dramatically. In its third quarter