Issue:
After adding licenses to the VMWare License Server the number of licenses reported in Virtual Center do not properly reflect what is in the license file. For example, some Features may report 0 Remaining, and 0 Total licenses when there should be a current license count available.

Using the license checker from the VMWare website correctly shows the number of licenses. http://www.vmware.com/checklicense/ This verifies that the license file(s) are good and correctly formatted. You can also use this tool to combine multiple license files into one.
Solution:
Unfortunately adding licenses to the VMWare License Server requires a particular procedure to be followed. The correct procedure is listed below.
To upload a server-based (centralized) license file:
1) Open the VMware License Server Tools
2) On the Menu Click Mode
a. Select “Configuration using services”
3) Click the Config Services tab
a. Note the setting for the “Path to the license file option”
i. Default: “C:\Program Files\VMware\VMware License Server\Licenses”
b. Copy your new license file to this location.
i. You can have multiple License Files in this directory, or combine the license files into one file.
ii. Make copies of any original files and store in a different location before combining.
4) Click the Start/Stop/Re-Read tab.
a. Click Stop Server.
i. You don't need to wait for it to stop
b. Click Start Server.
i. Make sure “Server Start Successful” appears at the bottom left corner.
c. Click Re-Read License File.
i. Wait for “Reread Server License File Completed” to appear at the bottom left corner.
5) Close the VMware License Server Tools
6) Click Control Panel….Administrative Tools….Services
7) Restart the following services for
a. “VMware License Server”
b. “VMware VirtualCenter Server.”
8) Log in to your VMware Virtual Infrastructure Client 2.0
a. Click Administration
b. Click the Licenses tab to confirm your licenses.
To add licenses to a NEW ESX Server
1) Log in to your VMware Virtual Infrastructure Client 2.0
2) Click the Inventory Button
c. Select the ESX Host server
d. Click the Configuration tab.
e. Under Software, select Licensed Features.
i. Ensure you have selected Use License Server and your fully qualified domain name or IP address is listed under License Sources.
ii. Under ESX Server License Type, select ESX Server Standard