When player connects to the server, and the location where the player will spawn is has a single solid block with air below (such as elevated block), the player will briefly fall though the block (visually), then the correct position will be set.

The issue can not be reproduced on single player 1.8.x Minecraft client, but does occur in multiplayer 1.8.x when connecting to Spigot 1.8.7 build.

The issue has occurred in prior builds of Spigot 1.8.x.

For purposes of testing, Bungeecord and Plugins were removed to eliminate their possibility to interfere with spawn point generation.

The problem does not occur if two blocks exist below the player. In this case, it was tested in air 50 blocks high, with two oak planks as the platform.

The problem did not occur on a teleport command, or warp command if using plugins for these purposes.