Steps to reproduce:

1-) Crowd 2.6 with Delegated Authentication Directory, with the following options activated:
a.) Delegated directory type: Microsoft Active Directory.
b.) Use Node referrals.
c.) Use Nested Groups.
d.) Sync users details.
2-) Confluence 3.4.6
3-) Then upgrade to Confluence 5.1.4
4-) The Confluence upgrade process finishes correctly, but no one who belong to the Confluences-administrator group through a nested group is able to see all the Spaces, and when you check the new DB table [cwd_directory_attribute] the "usedNestedGroups" attribute is missing.

Workaround:

So in order to fix it you either insert manually this attribute in that table and set its value to true, or proceed creating a new Crowd Directory through the Users Directories menu in Confluence.