In order for CreateFromIntersection to map tables, the tables must have "matching" primary keys or unique indexes in both databases.
All tables and views should appear in the mappings collection if the names and schemata match up, but they may be ineligible for comparison.
Programatically, you can check the "Status" property on each mapping to see if the data in the mapped table or view will actually be compared. If not, then you can add primary keys or map manually. Please see the following KB for example code.
http://www.red-gate.com/support/Knowled ... apping.pdf