Today I saw a short line twice in the Geany-git by PPA that was built around 10 days ago, so the issue for short lines is still there. But I couldn't reproduce it. If I can reproduce it, I will mention it here and I will open a new issue at sourceforge.net.
When short lines starts to appear twice, then the top line of the editor is completely red (from the left border to the right border of the editor) for some seconds. A saw this behavior many times in the past.