- Inheriting permissions and inheriting roles are not the same.
- The Sharepoint GUI by default only breaks the permissions inheritance when you select "Edit Permissions" for an object or list.
- Removing permissions from a parent site or object with "Remove user permissions" will delete that user's permissions from all child objects, even those that have broken the permission inheritance.
Here's more detail on the subject:
http://kjellsj.blogspot.com/2008/10/sharepoint-acls-roledefinitions.html