When running Scene Builder Probe, I noticed that styling of selection handles is incorrect:
the shadow rectangle displayed over the selected object is replaced by a black outline.

it is like the selection-rect style class from Theme.css was unresolved in Probe.

.theme-presets .SBKIT-content-panel .selection-rect {
    -fx-stroke: null;
    -fx-fill: rgba(0, 0, 0, 0.05);
}

I double checked the following:

1) theme-presets and SBKIT-content-panel are set in style classes of content panel root
2) selection-rect is set in style classes of the selection handles