When I go through a way stone I usually have to disconnect from the server and join back in order to get the world to load.

Try reloading chunks with F3 + A?

I have never been able to replicate this issue. I am closing this for the time being, seeing as it most likely was some lag related issue. If it still occurs, re-open the issue and I'll make a quick fix by reloading the world on teleport.