I added plugins on the server (Spongeforge, LuckPerms, Nucleus, and a few others). When I got back on, I could not use the signposts (another mod that integrates with this one and was working well). I made my way to the village near spawn to use the actual waystone block, and I went to teleport to the other village. But it said I had not activated any waystones. (I had 4 activated before).

I think it's an issue with permissions, but I don't know what permissions to add to the default user. And it could be a thing where all the waystones got reset, which would not be cool. I'm hoping this is a question, and not a bug.

Well that is supremely weird. Bug not easily reproducible. I got to my second village and clicked on my waystone and all of my activated waystones were back on my list. Also, figured out why Signpost wasn't working. It was in the spawn protection zone.

I don't know why it said there were none activated. It is a bug, but it's a livable bug.

If you figure out a way to reproduce the issue let me know, right now I can only assume it's some weird compatibility issue with SpongeForge. If it does happen again, relogging should fix it as it seems the client is just getting out of sync with the server.

I had the same problem after I died on my server. I tried to use my warp stone after recovering my items but it said I hadn't discovered any waystones yet, even though I used one to get to where I was at. I made it back home, touched my base's waystone, and used my warp stone. All my other waystones then showed up on my list.

EDIT:
By the way, I'm using straight up Forge, not SpongeForge. Latest version for 1.7.10.

EDIT 2:
I reproduced this issue by loading a fresh world with just Waystones installed on 1.7.10 with Forge build 1.7.10 - 10.13.4.1614. Placed 2 Waystones, activated both. Gave myself a Warp Stone, tested it and my "discovered" Waystones showed in the list.

Then, I flew up high and entered survival to kill myself, and when I recovered my Warp Stone, it said I hadn't discovered any Waystones yet. I then can walk up, touch an already activated Waystone, and use my Warp Stone again. All the Waystones are then visible and I can teleport to any of the ones I've already discovered.

This test was done in Single player.

I wanted to add that this really isn't a livable bug, considering if you die with your Warp Stone, you can't get home with it until you find a new or existing Waystone. Kind of renders this useless.