I am hoping this is just a quick answer.
We are upgrading our confluence from version 3.2 up to 4.0.5. We have installed a new test server, upgraded, and moved all data over to the 4.0.5 version.
I notice that in our current production version of 3.2 that the People Directory does not list every user in the system. But in version 4.0.5, the People Directory is listing every person.
Why is this?
Please note: The database on our 4.0.5 is a match of our 3.2 system, as we imported it, then upgraded on our new server, so the amount of users match, or is at least close enough for government work.
Also, we are not using any type of external LDAP, or Active Directory to populate our users, we create them all manually.
I suppose this is quite a late answer, I have been crawling through old unanswered threads, so putting my comment here in case it helps someone later on.
First I'd rebuild indexes so that we can make sure all users are indexed: https://confluence.atlassian.com/display/CONFKB/Rebuild+the+Content+Indices+from+Scratch
If this still does not give a positive result, I'd try to log in with a missing user to Confluence, then see if the user is being listed afterwards. The reason for this is that the related USERINFO entry (which the index works on) is only created upon first login. Given the fact there was major version change, I suspect this to be the root cause.
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