I experienced this around Ike. I raised the apoapsis to about 40km, with the apoapsis about 10km. I was waiting to get to the ascending node to get coplanar with my return vessel, but noticed my periapsis was chasing me. I wasn't sure if it was something to do with Duna's gravity, or a bug. So i switched to the return vessel which was in a ~50km circular orbit and observed the orbit was stable. When I switched back to the landing craft it was on a crash course, and just about to reach the apoapsis of about 20km, which is nothing like the 10km/40km orbit it had 20 seconds ago. Luckily I made a quicksave on the ground of Ike which I reloaded. Upon launch it was doing the same thing again, so I decided to burn straight towards an intercept with the return craft. It seemed like once I got above 30 km or so, the orbital parasite seemed to die, and Jeb, Val and Bob made it safely to the return vessel. Praise Kerbol.