I have the same issue with contracts. In fact, it seems that contract objectives are reset when you stop pointing the ship embedding the experiment. For example, there is the same issue if you go back to the space center during the experiment or if you switch between the ship and the space station during the docking maneuver. I didn't have time to try it yet, but i think if you right click to the command pod of the ship and choose "control from here" before undocking, the focus will be set to the ship and not to the station after undocking, and the objectives will be preserved