I'm using SciTE 3.6.6 (compiled for GTK+ 3.18.9) and the black square on the right corner between the scrollbars has reappeared again since some time. Initially on opening SciTE all is fine but often after some minutes I'm seeing that the area got black again.
Selecting text causes this and tracing it down reveals that its the call to gtk_selection_owner_set in ScintillaGTK::ClaimSelection that claims the primary selection. Comment the gtk_selection_owner_set out and the colour change does not occur. It doesn't appear to be a response to a selection signal as removing those connections has no effect.
Fixed with 4.0.0.