Your WHERE clause is converting your LEFT JOIN into an INNER JOIN.

You need to change your query a little bit.

Here's a nice article on the subject: http://www.sqlservercentral.com/articles/T-SQL/93039/

SELECT Users.Code AS FE

,COUNT(Matters.FeeEarnerRef) AS No_of_Matters

,ISNULL(SUM(Usr_Int1.Estimated_total_fee), 0) AS Fee_Estimate

FROM Users

LEFT JOIN Matters ON Users.Code = Matters.FeeEarnerRef

AND created > '2014-03-16'

INNER JOIN Usr_Int1 ON (Matters.Number = Usr_Int1.MatterNo)

AND (Matters.EntityRef = Usr_Int1.EntityRef)

WHERE (users.feeearner = 1)

AND usertyperef <> 7

GROUP BY code

,usertyperef

ORDER BY code

And you don't need the HAVING clause, it could easily go into the WHERE clause.