May be related to RT-26562

See the video here: http://www.screencast.com/t/QdBxJnmST

Follow the mouse pointer and note the overlapping controls that magically adjust.
See how the layout of GridPane adjusts the width of the columns while mousing over a TitledPane that is spanning both columns when there is no need for any adjustsments.
Note how the knob on the Slider overlaps the TextField in the row above in the GridPane.

In short - layout is initially wrong and is recomputed to various states of wrong in reaction to hovering on various components. There do not appear to be any size changes during hovering that would account for the re-layout or the different calculations of the layout.