Since about 1.6 I have had this problem. I built the beacon block and built the pyramid out of gold and iron blocks. The effects of the beacon still work and it has the right range. Whenever I leave the area and return or even just walk into my base the Beacon freaks out and the large beam flutters and turns on and off. The only way I can fix it for a second is by pausing the game and returning to the game, but after a second the problem comes back. Please try and look into this.