Server is running the latest version of Spigot, I just installed the latest version a few hours ago. All plugins are disabled when running this test (and all are up to date when they are not disabled). CraftBukkit version git-Spigot-0f17cfb-c1462a2 (MC: 1.11) (Implementing API version 1.11-R0.1-SNAPSHOT)

On some (usually rare) occasions, Shulker Boxes of any color, upon placing, become 'reset'.
It sometimes random, but on the server I have found specific spots/areas where this issue can be repeated infinite times.

Usually the items in the shulker box, along with any "named" shulker box text will be removed once the Shulker box has been placed. This will not happen until the box has literally been placed. On very few occasions has the shulker box reset to the default "purple" texture (I have not been able to duplicate the color-switching, but my players have reported it very few times).

I can assure you everything is up to date, and there shouldn't be any server plugins conflicting, because as I mentioned, during this critical test, all plugins were completely disabled.

I found this video on YouTube showcasing the same issue we are having: https://www.youtube.com/watch?v=kf_BDpiEE1k