It only happens when Geany is the top layered window, so far. So the lag might be related to windowing or the GNOME Desktop.
We have basically eliminated anything that has caused that sort of lag on other systems, so yeah it comes down to your system.
Unless it happens to another contributor who can check CPU (eg by top or system monitor on another screen) and then provide backtraces there isn't anything much we can do at the moment.