In Designer if a Query transform has lookup functions (wizard) that return columns and there is a Table Comparison directly after the Query transform then those columns returned by the lookup cannot be pulled down into the Compare Column list of the Table Comparison transform.
Source -> Query -> Table Comparison -> …
The work around is to put a new Query transform before the Table Comparison with straight mappings from the original Query transform.
Source -> Query -> Query -> Table Comparison -> …
Isolating the Query transform with the lookups seems to be necessary. Strange bug.
eganjp 
(BOB member since 2007-09-12)