I don't think I've seen this, but I don't do a lot with anchored objects, and I'm not certain what you mean by locked in this case. Did you already overwrite the CS5 version? If not, export it from CS5 to .idml and open that in CS6. If you have, try exporting from CS6 and see if it helps.
If neither helps, I think we'll need more details about the file, and perhaps an actual sample file to look at.
Thanks, saving the converted CS6 documents back to .idml files then re-opening in CS6 seems to cure the problem. Bit of a hassle with 4 books of 400 odd pages with multiple chapters and hundreds of linked images but will only have to do it when there are image updates etc.