1st, I have to say I'm not sure if this is something solely within CEDET, or due to something ECB is triggering. I'd appreciate any thoughts.
Once in a while I find some background activity trying to kill buffers. I notice this most often when emacs -- for no obvious reason -- pops up the prompt like "file <X> modified. do you really want to kill it?" The most aggravating symptom is when I'm ediffing files, and ediff announces "You have killed a vital Ediff buffer---you must leave Ediff now!"
I'm guessing something in the fine CEDET family of tools thinks *IT* has scooped up a particular file for parsing, then parses it and attempts to clean up after itself, not realizing its cleanup efforts exceed its scope of work.
I can collect and share more details, if anyone's curious.