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.
Related issues
Attachments
Comments

[media][media]

Confirmed, you need a 2 level pyramid for "Jump boost", but after removing the second level you still get jump boost.

Confirmed in 14w02c.