If your join query is returning zero rows, then the MappingIds do not match the CustCode values.
If I try your code with pure strings:
List<string> mappings = new List<string>() { "A002", "A75", "B908", "123456", "672314", "756213" };
List<string> references = new List<string>() { "htg1", "EDDIE1", "EDDIE2", "A002", "A75", "B908" };
List<string> joinItems = new List<string>();
joinItems = (from d1 in mappings
join d2 in references on d1 equals d2
select d1).ToList<string>();
Then I get what I expect: three strings "A002", "75", and "B908"
So ... start with the debugger, and look at exactly what your Lists contain, and what relation there is between the Ids and CustCodes - I'd suspect you want CustID instead of CustCode, but I have no access to your data, so I can't be sure.