This is using Blenders internal renderer? I've been rendering using that and don't remember having to take any extra steps, the material and texture setup should theoretically take care of it.
I'm afraid I'll only be able to help with this tomorrow since I'll be AFK, but try searching for mipmap settings, either in the system settings or the material.
The same method that fixes this issue on other engines fixes it for me so I'm currently using a script to convert the tilesets and it's probably for the better anyways since it seems to be an issue outside of blender even if it isn't an issue internally for everyone. I've also had to start unchecking transparent after setting the material to shadeless which I do not recall having to do before (I also recall the first time [before this shadeless issue], I tested this that it just worked without seams as well not sure if the two issues are related or if im just having a false memory though.
