Hmm, I just digging in the past and I discover the same bug in 2012, here in [#64](https://github.com/geany/geany/pull/64) and in [scite #1477](https://sourceforge.net/p/scintilla/bugs/1477/).
The way we solved this problem was to force the sci widget to be left to right by gtk_widget_set_direction(). This code still in [sci code](https://sourceforge.net/p/scintilla/code/ci/default/tree/gtk/ScintillaGTK.cx...) and in [geany code](https://git.geany.org/geany/tree/src/editor.c#n4857).
So I have no idea why we see this bug again.