Mod for me is working flawlessly in single player world with both vanilla blocks and modded blocks, but when joining a server it only seems to work with modded blocks and transmutes the the look of vanilla ones to a type of stair that is possibly waterlogged and breaking it drops the original item and I cant for the life of me figure out a possible work around or what the issue is.

I would need game logs to even have a slight clue as to what is going on, but even then I don't see how this could possibly be happening.
My only guess is that somehow the server has all the vanilla blocks blacklisted? I might need to add in code that synchronizes the blacklisted placements.