Ok good :) I think it is ok to use NULL are parent_id. That means it is the start of a serperate folder hierarchy and it allowed according to the content repository documentation (which is definitely out of date).
Actually cr_items.parent_id is definied not null. It doesn't have a constraint on it and it assumes items with no parent have parent_id of 0.
Maybe this is what seems wrong?
I'll have to look into this, and I might just create a root folder for all file-storage instances if I can't figure it out quickly.