sorry that it took me so long to get back to you.
While investigating your problem we came across a corner case that KNIME’s Naive Bayes Predictor handles slightly differently to other implementations and this took some time to adapt (please download 3.7.1 as once it is released - should be very soon).
Anyway, any other Naive Bayes implementation I tested always predicts the same class, or nothing at all 
. I’ll spare you the details.
You could try another classifier, as proposed by @DaveK, instead.
I’m very sorry that I can’t provide you with a proper solution to your problem.