This bug is simple enough. In the latest snapshot (and possibly earlier), ender crystals no longer show their 'beam' effects. Attached is a screenshot taken in the latest version, and a screenshot from the wiki. May be tied to MC-31649.
EDIT: Apparently not tied to MC-31649, as that was fixed and this is still an issue.
Bug still present in 13w41a. I guess it wasn't tied to the beacon bug after all.