YOu need to close any open editing boxes (AKA dialog boxes) - the game can not save if any are open because the changes made in those boxes do not update until the box is closed so if it allowed saving the esp while they were open you might lose data ! -- If you think they are all closed already check for any hiding behind other windows or go to the top and got to View - Open Windows and then in the popup box that opens close any windows that are displayed.
They are probably hiding behind one of the other menus. For some reason Bethesda decide not to include the standard Window controls in the CK.. Window -> Cascade would help a lot