I’m not sure if this is related, but navigating around the Grasshopper canvas has become very laggy recently too. For example, it struggles to move when I right-click and drag, instead bringing up the right-click menu.
The check box is ticked by default and can be unticked during a grasshopper session, but the untick is not preserved so when you next start grasshopper the box is ticked again. Version 2.1.4.0.
Unticking the check box does not remove the red and green boxes, nor does using Remove all highlights from the Pancake menu.