I am building out a new dev environment, and I just created a bunch of new indexers on brand new vm's. I also setup a search-head, and pointed it at my dev license mgr. So far, so good. However, when I setup distributed-searching, I am getting a "duplicate license" on the new search-head. All the new servers are pointing at my dev license mgr. I logged into my dev license mgr, and looked at the licensing and the distributed-searching, and I don't see that message anywhere.
Which version of splunk you are using? Have you checked that you have not added license on your search head?
Check if this applicable in your case - http://answers.splunk.com/answers/8475/distributed-search-issue-duplicate-licenses