Kevin,
When importing content, the items assume the same permissions as the collection into which they are imported. The permissions of the root collection are special as this collection does not actually exist. For that reason the permissions are taken from the module settings. However, whereas you can change and 'unify' permissions on a collection, the root collection cannot 'unify'. So your only option is to either (1) move all the content into a collection, set permissions in that collection and select 'reset permissions on all children', or (2) change permissions by hand. A third option would be to delete everything and start again and this time import into a scollection, or (if you really want to import into the root) set the module's permissions first.
For best-practice: it is best to import into an existing collection and not the root.
Peter
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