Hey BlueCorvid!
Sorry for the inconvenience! :(
The tiles should work with HexKit. Also sorry for the cascade of questions, but I hope we can fix the issue together! Which tiles are you trying to make work with HexKit? With a border or without one? Flat or pointy? What do you mean with "empty borders"? Can you post a screenshot of it looking weird?
Thanks for taking the time!
Steven