Try changing your copy and paste detection tool to IntelliJ (if you haven't already ;). I just ran it on our codebase and the results are simply staggering.
That's probably as much of a statement about our codebase as it is of IntelliJ's smartness, but it uses anonymizing of all names  (Class, Method, Variable whatever...) which finds those duplications you'd miss at first glance.
It also associates a cost , 'which is the arbitrary units being the code block size calculated using the additive algorithm; generally, the larger the code piece, the higher the figure'.
If the block is in the same class you can also go into that chunk of code and extract a new method from it wherein intellij destroys the duplicates automagically.
The fact that it anonymizes compilation units also means you can spot duplications which can be removed through parameterization - this is a significant step up from dummy duplicate detection.
It also has a sub-expression anonymizer aswell but this significantly slows down the detection process. I may try it overnight to see what joy it yields.
I'm off to see if I can get a LOC reduction bonus from my boss...