Hi all, looks like it has been a little bit since someone commented on this one, but I just ran into it as well. I'm running the latest version as of today 1.1.3, and the only mod I have is mechjeb (which, was not a component of the vehicle I was using). To try to troubleshoot what was going on, I tried repeating the exact same launch and actions repeatedly, with minimal changes, and each time it happened. I did get it to go away finally, after removing a single component from the vehicle. I had the AE-FF1 shroud, and was using it not far behind the command module (I have a picture of it). Once I removed the shroud, and did not change any other components on the ship, it didn't clone once I began an EVA.
I'm not sure if this resulted from a problem with the part, how the part was connected, or even perhaps something changed just by going back to edit the ship, I really don't know. But thought I would share this bit of data to see if it helps at all!
