When I first setup a Windows 2000 and then 2003 Server in our office using per-server licensing, we got the default 5-user CAL pack. I noticed that after 3 users logged in, the Server would kick out a notice that I had too many people has logged in. That's when I noticed that the Server was counting users twice - once for their login, and once for their computer... For example, if User X logs in from Computer Y, then both X and Y would show up as having used a license.
The only workaround I found was to disable the License Logging Service.
What was I doing wrong?