If you don't want links in alternate categories (ie: additional areas than their main category) you can quickly delete them all by using MySQLMan and emptying the table CategoryAlternates.
Or, you can use the SQL monitor in Links to enter the command:
DELETE * FROM CategoryAlternates
I don't believe you get a confirmation, or warning, so once you do it, re-index and re-build and it should work.
If you get an "error" of some sort with the command above, just do what it says. You want to DELETE FROM CategoryAlternates all the links. No other table needs to be touched.
http://www.postcards.com FAQ:
http://www.postcards.com/FAQ/LinkSQL/