You guys seem to be pretty far ahead in this matter, but just to help reproduce this: On a hunch I disabled FCOItemSaver, because as Baertram said, it adds a bunch of menu items, and I didn't really come across this issue anymore. While adding support for FCOItemSaver to my own addon, I had to reactivate it for testing, and the issue was there again.
Just to make sure the issue is isolated correctly. I really like FCOItemSaver and would like to make use of it again.