I've noticed that if you don't specifie where hudson has to look for the pmd result file it will look here: **/pmd.xml. This is fine however if you have somehow two pmd.xml files in that structure which are the same hudson will evaluate both. So for example you have a result in /target and one in target/site.
This leads that you have a duplicate overview. I did not notice / or test it with checkstyle findbugs or cpd (could be the same). I know that there should be not 2 result files in the first place but still it would be possible to check if there are two and if they are the same ignore the older one for example. Or make a hint in the documnentation / FAQ that a duplicate result could be caused by this.

I have running hudson with the version 1.347 and PMD 3.2.

For me i've fixed this by specifie the exact folder where to look.