The first issue I believe is caused by border tiles being on the edge of the 20x20 squares the tiles are saved it, due to the lack of the same tilemap in an adjacent border the game does not render any in the tile. You can see this error yours self by slowly making a line of tiles that have a border and tends to happen every 20 tiles (IE -10, -30 , -50 ect).
The second issue is when using the brush alpha setting with border tiles, the border edges use 100 alpha instead of using the value from the joined side.
