Searching full text data is a very complex task. SQL Server actually farms some of the work out to the Microsoft Search service running on the server.
You can try both the CONTAINS and CONTAINSTABLE functions as they work differently you may get different results from both of them.
How much data are you searching, and how complex is the search query that you are passing the query?
Is your join back to your regular table running correctly, and is that query indexed correctly?