Interesting. Ok so I had ED-E follow me, and Cass joined. I posted earlier that I was having trouble with ED-E glitching with the voice that came from the brotherhood, even though I killed them all...lame......., so I sent him packin back to 38 to wait.
I was in the process of doing a mission, and BOOM, Cass is gone. No idea what happened. Then I worked on a few missions, went back to 38 casino to rest, and they both appear after I sleep, WTF?
They stand there till I say follow me, then ED-E talks to me again, same guy from the brotherhood who is dead, and now a new guy from the followers, and all is well with the world.

NEW PLAN OF ATTACK PEOPLE!!!!: TO FIX ALL THE [censored]-TASTIC BUGS IN THE GAME, JUST KEEP PLAYING UNTIL THEY JUST SOMEHOW DECIDE FIX THEMSELVES! Or at least till your sick of all the bugs and you hit the forums to complain.

I killed all the BoS and I still had the quest text telling me to take him to Hidden Mountain (which I blew up as well). Didn't go away till I took him to the followers.

As for them disappearing I usually I had been wandering around and if I get on a rock (or something similar) and ED-E and boone would runoff to try and find a path up to me. It happens with enemies as well. I have also had them disappear just turning a corner. They have always comeback soon but it still is a little svcky waiting.

WHY IS ED-E SUCH A PROBLEM??!?!?!