I posted about this before but it hasen't been resolved and I'm running into it again.
I also found another side affect of this bug.
In a large library where none of the items are on the stage, if you rename a movie
clip or folder the items rename, but a duplicate is created with the old name.
Below, I renamed the Movie Clip by adding _test to the end.
The duplicate or the new name may be an empty MovieClip that you can not access
This also corrupts the timeline of the Movie Clip by creating duplicates of the existing layers.
Q suggested dragging the items to the stage before renaming as a workaround.
This seems to keep them from duplicating but I found that the Timeline still becomes corrupted.
By the way, all the library items were created in Flash and I even tryed to clean up the file by importing the library into a fresh fla.
I've seen this before. It happens when the symbol name has non-supported character or an ETX character. We have fixed this issue in CS5.5. I can take a look at your file. Please zip it, change .zip to .zzz, and email it to my attention at FlashAuthBetaBugs@adobe.com.
Also let me know which symbol is causing you issue so I can target those first. In the meantime, try saving your file as Flash CS4, does it still duplicate after you rename the symbol?