Recently began having problem with Pads Logic. Whenever I attempt to create or modify 2D lines the mouse poiinter is not visible in drawing area. Playing around I am able to accomplish this if I right-click first in the drawing area, then begin 2D operation. Sinialr problem in parts editor when I attempt to change pin name or number. I will note that I have a multiple monitor system. This shouldn't matter but may be worth mentioning.
Try changing your cursor style in Tools > Options > General from "Normal" to some other cursor such as "small cross" and see if that makes a difference when selecting Create 2D Line.