The context_id is assigned the parent_id of where you put your stuff in CR under (unless you explicitly assign a different context_id, which FS never does), e.g. a file placed under a folder will have a context_id equal to the parent_id = folder_id of the folder. Since the root folder must be placed under something, there is a magic entry "Page" in CR that is the "root of all root folders", and it's context_id is -100. Thus, all root folders will have a context_id of -100.
The permission hierarchy is taken care of by the package_id of the FS instance, which you can find in fs_root_folders. I think your problem is related to this thread.
