I don't see any issue. Of course I don't have exactly the same system as you, and I'm using Geany 2.0.
If it only occurs at some zoom sizes it sounds like its an issue somewhere in the rendering stack, Scintilla, GTK, Pango, Harfbuzz, or the fonts, lots of moving parts.
It _might_ be worth trying Geany 2.0 but I can't guarantee anything, the only part of the render chain it changes is Scintilla.