Jem it sounds as if Shila is still a bit anxious about being left despite having Isis.
I think i would probably go back to basics and start from scratch again, by leaving them for 5 mins and then gradually extending the time they were left so she really gets it that your coming back
Also i's make sure they were both tired before i left them for longer periods, by a good walk/play etc, in the hope that sleep and Shila forgets your not there. Maybe another trick would be to leave a radio on so she can hear some voices