I think ED-E has scripting issues for some. I've seen him take it upon himself to just start wandering through the wastes. I've had to chase him down, tell him to wait then follow again. If I use the console to reset his scripts he works fine again.
Have you tried the wait then follow thing? I'd assume yes.
I can give you console commands to reset him but you
have to remove all your things from his inventory or they will be gone!Open the console (~)
Click on ED-E so you see his name at the top center of the screen. Do not click on anything after that with the mouse! (Then type the following hitting enter after each one:)
disable
enable