Testing was done with a fresh copy of Minecraft 1.4.7 without any mods or alterations.
The End Portal does not render correctly on ATI graphics,
For some reason the extra layers are attached to the player instead of the portal. (this render issue also happens on any mod that uses the same effects)
This is also posted on the forums,
http://www.minecraftforum.net/topic/1665818-odd-render-bug-with-ati-graphics/
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kumasasa
Duplicate of MC-1607, please use the search function to see if your bug has already been submitted. Currently over 51% of tickets are being closed as duplicate.
I did search, but with over 100 topics you tend to only read the names and "ghost portal" didn't stand out as being the same issue 🙂
As a side note this report has far more info 😉
I don't know if the duplicates get looked at so I'll post over there.
kumasasa
Well, at least you did search... 😉