I think I know what you mean - but I'd be inclined to think that if there are visual problems with the tiles, it's a problem with the source image rather than WADE, as all it does is drawing that image onto the screen, it doesn't do anything special with it in terms of adding borders or resizing it in any clever way :)
I'm saying this from experience, having tried to create some isometric tiles before - it isn't easy. Depending on the graphics program that you use to create the tiles, it may do strange things with antialiasing on the borders. But there are ways to fix that.
Could you attach some of those tiles to your post (or otherwise send them to us via email), and I will try to create a simple isometric project with them (with a scrollable map) to see if there are any problems? I can then share this project with you so you can use it as a starting point for your own project.
Of course, if there is any problem with the way WADE uses these tiles, we'll try to fix it as soon as possible.
Admittedly the documentation for the JSON file format could be better. However the structure is pretty simple: the "terrain" object contains an array called "tileData". It looks like this:
"tileData":[ {"texture": "textures/water.png"}, {"texture": "textures/grass.png"}]
So it's an array of objects. Each of these objects describes a type of tile, and should have at least a "texture" property that describes which texture you want to use (you can add other properties to your tiles if you like too). In the above example, I have two types of tiles: water (element 0 in the array) and grass (element 1 in the array).
Then there is another property of the terrain, called "tileDataIds". This is a bidimensional array that describes how the tile types described above are laid out on the map. For example, a map with lots of water and some grass in the middle will look like this:
"tileDataIds":[ [0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0], [0,0,0,1,1,0,0,0], [0,0,0,1,1,0,0,0], [0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0]]
The same structure applies to transitions ("transitionData" and "transitionDataIds") and details ("detailData" and "detailDataIds"). For those, you can also use the value -1 to indicate that you want no transitions (or no details) in a particular place.
Anyway, please do send us the tiles that you're trying to use and I'll be able to tell you more about any problems that you're having.