I then compared teh two database tables using SQL delta and sure enough there are inconsistancies between the upgraded tables and teh clean install tables.
What I want to know is have any scripts been made which either sort out the tables so that they are teh same so I can export/import the data, or something which can copy teh data accross correctly?
If the old YAF version was v1.9.1.x or older, you have to use a special web.config (included in the newer YAF distributions) and migrate your data using YAF's installer, which will detect the old tables and migrate them. If your version is above 1.9.1.x then you can use the standard web.config included with YAF but you will still need to use YAF's installer to migrate the data and and table/stored procedure inconsistencies.
tha_watcha will be able to shed more light, as he is the DNN module author and will know of any 'special' procedures since you're running under DNN.
But normally on an upgrade (From the Install Wizard) should altered the tables correctly. Otherwise you should take a look at the tables.sql file which creates/alters the tables on install/upgrade.