Oh, trust us, we understand being busy 
.One thing to check: I imported the table structures in your package file and noticed that neither of your PKs are marked as Updatable (see attatched image). Are these keys both auto-incrimenting? If either or both of those columns are not autoincrimenting, I would try checking that check box and re-deploying the package to see if the problem persists. The issue may be that the DDT thinks it can't overwrite the values for those PKs and as such isn't overwriting the existing records as it should.
Unfortunately we can't test this definitievely on our development machines at the moment. We've recently updated the structure of the DDT package files and, as such, I can't deploy a DDT package created with the old version 
. We'll be releasing a new beta build within the next few days that will have the new DDT structures, so if the above idea doesn't shed any light on this, we can load that on your end, re-create the package, and then we'll be able to deploy it on our development machines and get a better idea of what is going on.