When you make a full beacon, then remove blocks from the pyramid that aren't part of the 3x3 on the top layer, it doesn't update and remove affects that are only available with larger pyramids.
MC-37972
Beacons Don't Properly Update
Resolved
Duplicate
1
Ezekiel
(Unassigned)
Confirmed
beacon, beacon-block, beacons, block, iron, refresh, update-failure, updated, updates
Minecraft 1.7.2, Minecraft 1.7.4, Minecraft 14w02b, Minecraft 14w02c
Retrieved
Confirmed, you need a 2 level pyramid for "Jump boost", but after removing the second level you still get jump boost.