I have got a problem where every time I upgrade to a newer version of Drupal, the settings from my custom modules are lost. So each time, after each upgrade, I have to redo the settings that come from these modules. It has become a hassle now as it is also affecting the taxonomy term associations this time around. After I upgraded my site from Drupal 6 to 7, the terms that have been entered in my own custom content type have been listed as Taxonomy Upgrade Extras. It's like the nid to taxonomy term association has been lost for the custom content types.
I would really appreciate it if anyone could help me figure out why it's happening or possibly provide a solution to it. Thank you.