This article applies to:
7.x Briefcase for Windows
6.x Briefcase for Windows, Contributor Pro
1) The items have custom permissions assigned to them in SharePoint. Custom permissions are not supported by Colligo as items can fail to appear after a sync.
2) The site or library was using anonymous access and/or is not inheriting permissions.
If you choose to disable anonymous access on the site, and there are lists (or libraries) configured so that permissions are not inherited, you may find that items in those lists still do not display. To ensure these items display, you need to temporarily enable permission inheritance on the lists, then disable permission inheritance, and reapply the specific permissions desired. Then users with permission to access the lists can see the list contents.
For more information around how anonymous access affects Colligo, see here.