In Dutch, there are also three words to answer a question. "Ja" ('Yes') and "nee" ('No') are used to answer standard questions the way one would expect. For negated questions, "nee" ('that is correct') and "jawel" ('that is not correct') should be used.
Sometimes people answer a standard question with "jawel" to indicate 'Yes!'. I'm not sure whether that is appropriate, but it causes no real confusion. What does confuse me (and often them) is answering a negated question with "ja".
On the other hand, it always confuses people when I answer their "Do you want coffee or tea?" question with "Yes" when I don't care, so maybe it's all my fault.