So, you have a layer set to Auto pilot,
then you play a clip in this layer, and switch to a different deck.
The clip ends and a new clip from the current deck is launched.
That's because you told the layer via the auto pilot setting, to launch a new clip when the currently playing clip has ended.
If you'd like auto pilot to stop on deck switch, you need to disable auto pilot, when you switch decks in Resolume 6.