Copy the :
where SplitEmpID is not null
check into both the inner queries so that it execs before the UNION A-L-L, not after.
If you at all can, change the GROUP BY in the second UNIONed query to be company first, so that it matches the other query and the outer grouping:
group by B.company_name,MediaGroup,companyid,splitempid,issyr, IssMth
) mastertable
SQL DBA,SQL Server MVP(07, 08, 09) A socialist is someone who will give you the shirt off *someone else's* back.