mickeko - are you using XP or Vista? If Vista, is UAC enabled? Using DeskScapes or DreamScene? Playing a video dream? Just takin some stabs... snapshots should definitely show the icons on them as well!
Currently I don't forsee having Fences allow for no-alignment (e.g. free-floating icons within them) primarilly as I don't have horizontal scrolling available at this time. perhaps at some point 
I do hope to have Fences be able to show folders on the desktop... imagine right-mouse-button-dragging a folder, and when you drop it, it creates itself as a fence on your desktop. (The first time you do it it'd show a menu and one of the options would be "create fence for this folder", and if you selected it it would ask "do this every time?"). Anyhow, this would be available on Vista only (not XP) due to tech limitations, but you could even have folders that show in details-view/etc
Interesting suggestion though, regarding "open folder IN the current fence"... i'll have to think about that one! noted.
thanks for the feedback!