I have had the same problem and have looked it up and haven't found a lot on it...
The problem is most likely is just that you are spawned really far from land? Check the concordance. Mine was at like (500,400) or so.
I found that was only one of the problems that i had, I also had about 25 enderdragons that where flying around that i'm pretty sure i couldn't kill them.
I'm not sure there is a fix but you can delete the end file and have it re generate the end... this fix my enderdragon problem at least.
Also I haven't done this yet but as i was reading what other people where saying and they just changed the spawn point to where it should be.
Version: 3.1.2
OS: Windows, 7 Home Premium
Java Version: Java 7 Update 9
Java Version: Jave 7 (64-bit)
I would love to know if there is a fix tho...