Since you have given us no table schemas, indexing, query plans, sample data, examples how the 2 queries differ in their output I can only say that when faced with the issue you have I break each query down into it's component parts to determine where my logic flaw resides. I also examine (and set up test data cases for, especially boundary and NULL/NOT NULL scenarios if appropriate) output differences very closely to look for reasons why the diffs exist.
Best,
Kevin G. Boles
SQL Server Consultant
SQL MVP 2007-2012
TheSQLGuru on googles mail service