When I press Ctrl J (or F) instead of the near ends of separate sections, their farther ends connect and create weird lines through the shape.
Why does this happen? (Blender 4.5 LTS)
Hi there. Yes, this quirk really annoyed me since they changed how strokes will be joined and it is still not as good as how it worked before. That said, here's some tips that will help you:
In edit mode, make the stroke direction visible. When in edit mode, go to your Grease Pencil Options overlays, and enable Stroke Direction
Joining strokes should happen between the last and first points of detached strokes, so this should allow you to see where you might have to flip the direction of a stroke. You can do this in edit mode by selecting the stroke, then going to your Stroke menu, and click on "Switch Direction"
Lastly, instead of selecting the points you wish to join, we now have to select ALL of the stroke we wish to join, then hit CTRL-J. Yeah - I find this annoying too, and sometimes, it will leave the original stroke or strokes behind. F will then close the shape.
Hope this helps!