The rainbow in the fancy skybox seems to track Minecraft's "View Bobbing", and wobbles in the sky when walking around. Disabling "View Bobbing" in the video settings makes the rainbow move smoothly across the skybox.

For reference, I am experiencing this on r1.8-310 with fancySkybox.normalWorlds set to true in the config, and I am playing in a regular single player world.

this is nearly unsolvable, the rainbows actually render with the sun/moon. If you watch close enough the sun and moon actually bob in vanilla.

See upstream issue: VazkiiMods/Botania#1705