Beacons refuse to work at a certain height in the End. I have not tested this in the Overworld or Nether.
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Since 14w32b, beacons need a clear line of sight up to Y=255 in the Overworld and Y=127 in both the Nether and the End, and ignores any blocks above that. Also the beam only travels to that height, so beacons above that height have the truncated beacon as shown here.
It seems odd for the beacon not to look for blocks all the way to the build limit.
Please switch to the default resource pack and see if it occurs there.