Kerbal Space Program

I am running KSP on Ubuntu 14.04 through Steam with manual execution of the KSPx86_64 program. The issue: On a flight to Duna, during stable orbit around Duna, I EVA the one scientist from the MPL to take an EVA status report. This works, however after logging the data, I can no longer select the Kerbal to control. "[" and "]" cause "Focus: ##### Kerbal" to be displayed but movement with WASDQE keys causes the RCS units on the ship to fire, not move the Kerbal. Furthermore, if I fire the engines, the Kerbal slides down the ladder but remains holding on to the ship. I left click on the hatch and select EVA hoping this will end the eva and I can continue to land on Duna. This however causes a second kerbal to EVA (There was only one kerbal on this ship when it left kerbin but now 2 are on the ladder). Neither can be selected by clicking or using "[]". Now, in addition to the kerbal cloning, the lack of ability to control the clones and end the EVA, I can still activate "Start Research" for the MPL which means another clone is still inside. (Also, if a clone is blocking the hatch, the next clone cannot exit through it.) I cannot return to the Space Center as I have kerbals on the ladder and I cannot get them off the ladder. Please suggest a way to repair.