In linux, the filename's case matters. was having issues with configuration, and figured out that I have two copies of configuration file

Waystones.cfg
waystones.cfg

Please update references to the file to match case in all instances.

Thanks for the hard work, and I do love the mod.

The upper-case version is the correct one. The config file is completely handled by Forge, so it could be that the other file came from an earlier Minecraft version (where it still used the modid instead of the user-friendly name). Unless a fresh install generated both of those versions, in which case let me know and I'll see if there's anything wrong with the Forge code.