One thing I can suggest is to do a restoration of just the eyes without affecting any of your morphs.  Select the eye and on the Preview window, right-click to call up the contextual menu.  Go down the list and highlight Restore, another menu will open, select Object to restore it to its default settings.  Afterward, you can manually reposition the eye to your intended pose.  Now the wonky eyes might be a crosstalking event with another morph you're trying to apply but I don't know if is the case with your problem.