Hi.
The bug is basically as stated in the title. When shaders are turned on, beacon beams generate behind the LOD's, so you can only really see them in the sky. However, beacons look normal without shaders.

Here's my Minecraft set-up for reference.

interesting. does this happen in the unstable development version? can download it here

Yes it does, but it loads in front of some of the further away LODs