When a row constraint in a GridPane specifies a valignment of BASELINE, the row is laid out higher than it should be, even intruding on elements outside the GridPane. Two consecutive such rows are also laid out much too close together. The attached FXML file gives an example. It looks a mess when you run it. If you remove the <rowConstraints> element, the layout is reasonable, but of course the CheckBox and the ChoiceBox aren't quite lined up the way you'd want them to be.

This looks similar to http://javafx-jira.kenai.com/browse/RT-11705, which was marked fixed a year ago.