Could be that it depends on the order, in which widgets are created. Could be similar case as with "second editor" pane option, where second pane is as primitive as possible in features, comparing to primary editor pane.
Not so much the order they are created, but probably the way they are arranged. Geany knows nothing about new windows that plugins add, so if they are placed in the widget tree where Geany thinks a "standard" window should be, it might well get confused. The split window problems are indeed due to Geany having no idea that this second editing widget exists or that it should do anything in it. There does not seem to be any simple short term solution to this.