Did you already do a clean reboot of the vCenter Server? This has solved some license count issues for me in the past.
If a reboot doesn't help it may be required to check/modify the database. Which database/version do you use for your vCenter Server?
We use Microsoft SQL Server 2008 R2.
Yes we restarted the VCenter felt 100 times.
What you mean exactly with modify database ?
For Example I have already checked with LDAP if the IDs are under "Licenses" are also coupled with the IDs in the table "VXN_Entry".