I'm not 100% sure if I've narrowed down the correct cause, but I think I have.
As of recent NL versions, in clear physics mode, objects are drawn in a solid, shifting color instead of their normal colors, to help them stand out more.
This works fine in all cases when unpaused. If you pause the game and then enter clear physics mode, this works fine. However, if you enter clear physics mode first, then pause the game, this is where it gets weird - the color doesn't update, until you advance a frame, at which point it suddenly jumps to whatever color it'd usually be at that time - but remains frozen on that one until you advance frames again. (In levels where scrolling is required, I suspect that scrolling would also have the same effect as frame-advancing if the high-quality minimap is not in use.)
Fixed in commit 33837a8.