"The projection angle of an isometric map is determined by the tile width and height you choose when creating the map.
The width and height you pick in the New Map dialog basically need to match the base of your isometric tiles, not their full image (though you should pick the full tile image size in the New Tileset dialog). For the isometric example map, this meant tile width of 64 and tile height of 32 pixels.
If you get small renderings errors at the edges of your tiles, this could mean you're still one or two pixels off from how your tiles are supposed to be used.
So for this tileset, when creating your new map, set the tile width to 64 and tile height to 32. When you create your new tile set, set the height and width both to 64.
Tiled:
"The projection angle of an isometric map is determined by the tile
width and height you choose when creating the map.
The width and height you pick in the New Map dialog basically need to
match the base of your isometric tiles, not their full image (though
you should pick the full tile image size in the New Tileset dialog).
For the isometric example map, this meant tile width of 64 and tile
height of 32 pixels.
If you get small renderings errors at the edges of your tiles, this
could mean you're still one or two pixels off from how your tiles are
supposed to be used.
Best regards,
Bjørn"
source: https://groups.google.com/forum/?fromgroups=#!topic/mapeditor/U2ZjbuzlVhY
So for this tileset, when creating your new map, set the tile width to 64 and tile height to 32. When you create your new tile set, set the height and width both to 64.