We are attempting to collaborate with NGUI but are running into some strange problems. I have committed to svn the NGUI project for others to work with. When the person pulled down the latest the UIAtlas behavior was missing from the prefab, the shader was gone, etc. Not sure if this is a Unity problem, but it only seems to effect NGUI prefabs. We have seen similar issues with corruption of NGUI assets.
Any ideas as to how this might be occurring?