It 'may' be possible to get a re-bill for the correct license or an internal license change depending on what needs to be changed. Is the root cause of the issue a Server vs Workstation license count? If yes, how many servers do you have, how many workstations?
Originally I was licensed for 35 "workstations" and 1 "management server" although my "Help then About Shavlik Protect" from the console describes these as "machines" or "seat counts". A machine or a seat could be either server or workstation. I only scan about 30 workstations. The additional 10 licenses that were purchased needed to be "server" licenses to scan 8 servers. I have some cushion licenses.
To answer your question: Is the root cause a server vs workstation license count? - I think so - My most recent purchase of 10 additional licenses needed to be "server" instead of workstation.
I asked my reseller to "exchange" them due to my sales person not explaining the licensing and providing the workstation SKU. I've been told Shavlik does NOT exchange or return licenses, but I'm more than able to purchase the needed 10 server licenses with the maintenance.
You should be contacted shortly with some options. Let me know if this doesn't happen in the next few days.