The active user count for JIRA is calculated by counting the number of memberships for the "jira-users" group.

It has been noted in some support cases that there exists memberships to this group for users who no longer exist in the user base table, causing a similar message to be displayed in the User Browser:

There are currently 5 total user(s) set up in JIRA, of which 6 are active and count towards your license limit.

We should probably fix the counting to only count users who exist. This could slow things down though.