Hi,
Since you need to import value into a field which is referred by a flat look table, you need to map the values of that field to the values maintain in flat look up table.
You can do the mapping from "Map Fields/Values" Tab.
You have probably Mapped Source fields with destination fields, but in case of importing values in lookup fields you need to map Source Value with destination value.
Keep the cursor on the required lookup field in Source field section, below that section you will be able to see Source Value section perform the mapping in that section too and it will resolve your issue.
Regards,