I had this weird problem when my Japanese and Chinese IME stayed in my IME list even though I had removed them. It was driving me nuts, but it turns out that they can be disabled through the dconf-editor
sudo apt-get install dconf-editor
Bold options are options that have been modified. The interesting one is the row labeled “sources”. Clear the entries of the IME’s that should not appear in the list and that should remove the IME’s that shouldn’t be appearing.