With the new version of KNIME there is still an old bug with WEKA integration. Option selection trees in WEKA classifier nodes' option dialogues (choose button) are still empty.
Also - there is still no access to override WEKA classifiers' parameters with flow variables.
But, could you please provide some more details, e.g. which weka-node is affected? Because for meta-classifiers like 'Bagging', 'RandomCommittee' etc. everthing seems fine, as far as I can see.
The problem is fixed and probably available with 2.10.1. This issue should only concern weka nodes where a NearestNieghbourSearch algorithm has to be selected. All nodes that require the selection of either a Classifier, Clusterer, Associator, SearchAlgorithm or a BayesNetEstimator should work fine. Can you confirm this?
Are there other nodes with the same problem (except those that require the selection of a NearestNeighbourSearch-algorithm)?
An issue regarding the flow-variables support of Weka Nodes has been created and is in progress. I will post a note after the target milestone is defined.