I decided to try again to give you more info. I used those cleaning options again and I've noted which folders have their sizes and locations reset to default, and which don't:
Pictures and Documents go back to default.
Music, Computer, [user folder], Control Panel, etc. don't go back to default.
So that's what works and what doesn't work with "Window Size/Location Cache".
Now onto the "Custom Files and Folders" cleaning option:
As far as I can see it didn't do anything this time round. Column widths and View type (details, icons, etc.) I don't think changed in the slightest.
So to sum up, the "Window Size/Location Cache" cleaning option works haphazardly at best and the the "Custom Files and Folders" cleaning option doesn't seem to work at all. At least for me it doesn't. I'm not sure about how it works for others with Vista.