Linux 64 bit.
Relevent part of the log
IsolatedStorageException: Could not find a part of the path "/home/coteyr/.local/share/Steam/SteamApps/common/Kerbal Space Program/GameData/AutomatedScreenshots/AS_Settings.cfg".
3484342- System.IO.FileStream..ctor (System.String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize, Boolean anonymous, FileOptions options)
3484501- System.IO.FileStream..ctor (System.String path, FileMode mode, FileAccess access, FileShare share)
3484602- System.IO.File.Open (System.String path, FileMode mode)
3484660- ConfigNode.Save (System.String fileFullName, System.String header)
3484729- ConfigNode.Save (System.String fileFullName)
3484776: AutomatedScreenshots.FileOperations.SaveConfiguration (AutomatedScreenshots.Configuration configuration, System.String file)
3484903: AutomatedScreenshots.Configuration.Save ()
3484948: AutomatedScreenshots.MainMenuGui.GUIToggle ()
3484996- KSP.UI.Screens.ApplicationLauncherButton.OnFalse (UnityEngine.EventSystems.PointerEventData data, CallType callType)
3485115- UnityEngine.Events.InvokableCall`2[UnityEngine.EventSystems.PointerEventData,KSP.UI.UIRadioButton+CallType].Invoke (System.Object[] args)
3485255- UnityEngine.Events.InvokableCallList.Invoke (System.Object[] parameters)
3485330- UnityEngine.Events.UnityEventBase.Invoke (System.Object[] parameters)
3485402- UnityEngine.Events.UnityEvent`2[UnityEngine.EventSystems.PointerEventData,KSP.UI.UIRadioButton+CallType].Invoke (UnityEngine.EventSystems.PointerEventData arg0, CallType arg1)
3485580- KSP.UI.UIRadioButton.SetState (State state, CallType callType, UnityEngine.EventSystems.PointerEventData data, Boolean popButtonsInGroup)
3485720- KSP.UI.UIRadioButton.ToggleState (CallType callType, UnityEngine.EventSystems.PointerEventData data)
3485823- KSP.UI.UIRadioButton.UnityEngine.EventSystems.IPointerClickHandler.OnPointerClick (UnityEngine.EventSystems.PointerEventData eventData)
3485961- UnityEngine.EventSystems.ExecuteEvents.Execute (IPointerClickHandler handler, UnityEngine.EventSystems.BaseEventData eventData)
3486091- UnityEngine.EventSystems.ExecuteEvents.Execute[IPointerClickHandler] (UnityEngine.GameObject target, UnityEngine.EventSystems.BaseEventData eventData, UnityEngine.EventSystems.EventFunction`1 functor)
Looks like a case sensitivity issue the real path is
/home/coteyr/.steam/steam/SteamApps/common/Kerbal Space Program/GameData/AutomatedScreenShots
Big S in "Shots"