I've been having this same bug every single time I EVA since I updated to 1.1.3. I've got the Kerbal Engineer, PlanetShine, and RCS Build Aid mods. I just found a workaround that kind of helped me out (this time anyway). When the bug occurred, I Alt+tabbed out of the window then back into the game again. This time Jeb still appeared to be outside my craft, but I could return to the tracking station without having to revert to an autosave.