All in all, brilliant idea and for a beta I'd say it's pretty solid. A few points I'd like to mention.
Issue One:
Not sure what to categorize this as (incompatability with another program, probably), but hopefully something can be done about it.
I have a dual monitor machine with different resolutions on the monitors. Thus I have separate wallpapers on each monitor, and different settings (center on one, stretch on the other).
Fences overrides this when it starts up and uses the primary wallpaper and wallpaper setting on the secondary monitor as well. I use UltraMon for the wallpaper setup.
Issue Two:
This may have been mentioned, but being able to configure fences to auto-add files of certain extensions to specific Fences would be real nice. So that when I add a new .txt to desktop, it automatically gets moved to the Fence I've configured to handle .txt files.