My church uses Jomsocial component (added on to Joomla) as the database for our church directory information. The set-up is pretty slick as each person's information is stored in their user profile and they can edit their own directory information they need to (well, they could - but usually it is our secretary that does so via her administrator access.)
Unfortunately, just as we got everything set up the way we wanted and tried to export everyone's information, we discovered that a number of records were not being included in the exported data (we use the Import/Export User Data For JS plugin from www.joomlaxi.com for exporting in CSV which we then open in Excel and merge to a Word template.) After a whole lot of looking around in the Joomla admin area and also in the site's database, I noticed that the records not being exported belonged to users who had been assigned to custom groups in Joomla 2.5's ACL system.
A google search based on a number of different phrase combinations did not bring up any exact solutions to this problem, but my eye did catch a reference to Joomla 1.5's user types being deprecated. This lead me to fire up phpMyAdmin to look at the user types assigned (in the jos_users table) to the users who were MIA from the exported file. In doing so I noticed that none of their user types (which survived this site being migrated from Joomla 1.5) matched any of the names of the Joomla 2.5 groups they were assigned to. As a test I emptied the usertype field for a couple of these users and tried another export. Le voilà, those users were no longer missing from the export. I then went back into phpMyadmin and emptied out every user's old usertype and as expected and worked hard for, everybody is now showing up in the export!
Remember, if you are experiencing the same problem as us, don't forget to back-up your complete Joomla database before you start monkeying around with it in phpMyAdmin. If you don't feel confident to do so, I'll be happy to have you hire me to do it for you.
P.S. - I did consider simply removing the usertype field from the jos_users table, since that setting is deprecated in Joomla 2.5, but I chose to simply leave it with all blank entries just to be safe.