networkin,
If I understand you right, I think you can right click on desktop, go to Configure Fences > Tools > More options (in bottom left corner).
This gives you an option to run the start-up clean-up wizard again.
HTH,
-t
EDIT: Didn't really read your #2 comment, seems you go the auto stuff sorted out. Again go to Configure > Organize and sort by type, name pattern matching, etc.