Ok, I reproduced it on your demo, it does not give a problem.
I tried messing around a little copying on the Demo what I did on my site: changing the order of the characteristics, changing their names, changing their values names, applying discounts, it did not reproduce the problem on backend.
But on my backend, with the product page it allways shows two lines for each characteristic with on one line a dropdown possibility to choose the value and the other line saying "no values found", so I gather when I save this "no values found" is saved too and another column is added.
The "no values found" characteristics are assigned the same ID number on the product page backend, so the characteristic "Uren scriptiehulp" has about 10 lines with the same ID all saying "no values found" except one line with the values accorded to them.
Shall I make an administrator user and mail you the login so you can have a look?
The problem started last week, not sure exactly when
Damiaan