This was caused by updating the server from 1.8.9 to 1.10.0, we did several tests on 3 computers and the server does not spawn these unless you update to 1.10.0. They appear over the entire map except for the spawn region interestingly enough and cause extreme lag, and go straight through the world below bedrock.

I saw a post somewhere mislabeling this as an Intel Graphics issue, but as we used several different systems with different graphics cards and processors, as well as many players to test first hand in our world we know this not to be the case as it effects every person who joins the server, which is about 20 give or take.

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Some notes that may help: A year or so ago there was a mod Pixilmon on it that is no more and was deleted and updated since last year and still worked fine and never had this issue. Possible block id corruption causing non-physical beacon spawns?

Beams disappear after some time if you don't move much but re-appear as you walk around.