Unfortunately, a bug crept in regarding the Experimenter in combination with cross-validation. Instead of summing up the differents folds of a run, they're listed as separate "classifiers" (prefixed with a number).
There a two ways to fix this:
Drawback: you have to do that whenever you select a new experiment.
This fixes the wrong indices in the default Experimenter.props file in the weka.jar archive.
Sorry about that, new versions of Weka will be released in the near future!