Well deepspace, you are correct. It appears that the area.sql file (should be located in the topo process directory) isn't being run. If it were some of the items you have would have been deleted and there would have been an MP_TYPE column. Do you have topo process in a completely separate directory from the map files? If not I'd suggest you redownload it and make it in a separate directory.
Secondly, in the topo_process directory can you open up area.sql in notepad and make sure it looks like this:
ALTER TABLE nhd_area ADD COLUMN mp_type character varying(50);
ALTER TABLE nhd_area ALTER COLUMN mp_type SET STORAGE EXTENDED;
ALTER TABLE nhd_area RENAME COLUMN gnis_name TO name;
DELETE FROM nhd_area WHERE fcode = '53700' or fcode = '30700' or fcode = '31800' or fcode = '34300' or fcode = '34305' or fcode = '34306' or fcode = '36400' or fcode = '37300' or fcode = '56800' or fcode = '43100' or fcode = '45400' or fcode = '45401' or fcode = '45402' or fcode = '45403' or fcode = '45404' or fcode = '46100' or fcode = '48500' or fcode = '40300' or fcode = '40307' or fcode = '40308' or fcode = '40309';
UPDATE nhd_area SET mp_type = '0x28' WHERE fcode = '31200' or fcode='44500';
UPDATE nhd_area SET mp_type = '0x49' WHERE fcode = '33600' or fcode = '33601' or fcode = '33602';
UPDATE nhd_area SET mp_type = '0x3b' WHERE fcode = '36200' or fcode='39800' or fcode='45500';
UPDATE nhd_area SET mp_type = '0x49' WHERE fcode = '46000' or fcode = '46006';
UPDATE nhd_area SET mp_type = '0x46' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 15;
UPDATE nhd_area SET mp_type = '0x47' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 10 and areasqkm < 15;
UPDATE nhd_area SET mp_type = '0x48' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 2 and areasqkm < 10;
UPDATE nhd_area SET mp_type = '0x4c' WHERE fcode = '46003' or fcode='48400';
DELETE FROM nhd_area WHERE mp_type IS NULL;
Let me know if it does or doesn't look like that and we'll work from there.
Here is area sql un edited by me, looks fine:
ALTER TABLE nhd_area ADD COLUMN mp_type character varying(50);
ALTER TABLE nhd_area ALTER COLUMN mp_type SET STORAGE EXTENDED;
ALTER TABLE nhd_area RENAME COLUMN gnis_name TO name;
DELETE FROM nhd_area WHERE fcode = '53700' or fcode = '30700' or fcode = '31800' or fcode = '34300' or fcode = '34305' or fcode = '34306' or fcode = '36400' or fcode = '37300' or fcode = '56800' or fcode = '43100' or fcode = '45400' or fcode = '45401' or fcode = '45402' or fcode = '45403' or fcode = '45404' or fcode = '46100' or fcode = '48500' or fcode = '40300' or fcode = '40307' or fcode = '40308' or fcode = '40309';
UPDATE nhd_area SET mp_type = '0x28' WHERE fcode = '31200' or fcode='44500';
UPDATE nhd_area SET mp_type = '0x49' WHERE fcode = '33600' or fcode = '33601' or fcode = '33602';
UPDATE nhd_area SET mp_type = '0x3b' WHERE fcode = '36200' or fcode='39800' or fcode='45500';
UPDATE nhd_area SET mp_type = '0x49' WHERE fcode = '46000' or fcode = '46006';
UPDATE nhd_area SET mp_type = '0x46' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 15;
UPDATE nhd_area SET mp_type = '0x47' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 10 and areasqkm < 15;
UPDATE nhd_area SET mp_type = '0x48' WHERE (fcode = 46000 or fcode = 46006) and areasqkm >= 2 and areasqkm < 10;
UPDATE nhd_area SET mp_type = '0x4c' WHERE fcode = '46003' or fcode='48400';
DELETE FROM nhd_area WHERE mp_type IS NULL;