It appeared at first that the position of 2 tile wide structures/features was off for the bottom half and potentially other structures on the bottom half as well. Annoyingly, FlaME doesn't support manual fraction-of-a-tile positioning so I converted to the dreaded .lnd.
Using editworld, I have been able to see that every single object below the half way point in the map, is shifted 1/128th of a tile to the left and 1/128th of a tile up from where it should be. Which is causing the following effect:
In-game, player structures will automatically snap to posistion in order to fill tiles correctly. Features however, will remain in their exact position (a feature I like) however, the hit boxes will snap to their tiles just like player structures. Causing the player structures to match with their moved hitboxes and the features to not. Causing things like this:

Falling back to a previous version of FlaME probably had no effect due to the map data remaining the same. Placing objects anew in the older version would probably work, it would be quite tedious, but fortunately, this only really has an effect on 2 tile wide/high structures/features. So your best bet is to open the map in an older version and replace each of the structures/features in question, in the bottom half of the map.
My question though, is the bottom half the half that you placed by hand? (in which case, the placement in the first place is the problem)
Or is the bottom half the half that you mirrored? (in which case, that is probably what is at fault)
"...If pure awesomeness were bricks, this would be the Great Wall of China...
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