To fix the issue you can do Finally I've found the reason of the problem. This part was wrong, because Projection was accessed inside the Elapsed delegate. But by that time Projection has already changed its state, which resulted in wrong coordinates.
This might help you For the blinking, see this post - it may be a bug in the overlay system. With the jagged lines, they do appear to be antialiased in your screenshot, but may have been scaled up. From experimentation, I believe that overlays are rendered to a separate bitmap for discrete zoom levels and then rendered over the map view scaled up or down to suit the current zoom level. So it may be that your overlay looks a bit rough at that level but zooming in or out a bit improves it.
hop of those help? Your timestamps are offset wrong, e.g. ...setpts=PTS+5/TB[ovr1]; but [0:v][ovr1]overlay=0:0:enable='between(t,0,5)'[base1];, so the stream starts after the overlay enabled range. It should be setpts=PTS+0/TB. Reduce all offsets by 5, similarly.