I have the same problem! When I first downloaded pencil 2D, this happened to me and I tried to unsnapping my timeline to see if that would work, but it did not. Now, I cannot seem to snap the timeline back onto the bottom of the window (it just disappear off screen). I also tried resetting the window and snapping the timeline at the bottom, but it did not work. I think it is because pencil 2D is too big for your computer. They have to fix this because now I’m doing animations with a floating timeline.