Hi Franklin - did you just re-import the tile set a number of times or did you do anything else to get this working? I have the same issue.
EDIT: I think I've found the cause - the terrain tiles work when using the default 'Base' layer, but it looks like applying them on a user-made layer shifts them a bit for some reason. I can use this to workaround the issue but I suspect that this might be something to do with the Hex Kit itself.