In the GUI, you can right-click on a top-level object and select update Permissions. This will then recursively update all subfolders for that object. It may take a while, but it will do it. You have to do this separately for depot objects, component templates, jobs and the other objects. The only object type that you can't do this with is for devices (I am assuming BladeLogic 8.0 here), but you can only have a folder depth of one for devices anyway.
Actually, what I realized about 10 min after the post was that in the pre-8.0 releases, the funtion only works when selected objects in the right-side pane. It doesn't work recursively when selecting a parent folder in the left pane -- actually, i knew this but had since forgotten.
In either case, this is resolved.
Right click on one of the folders and choose ‘update permissions’ ?