Did you use the following procedure before uninstalling IP 3.1:
1 - Start IP > Tools menu > Restore all Icons > click "Yes" in pop-up dialog to confirm > click "OK" to complete process.
2 - Repeat step #1 for the "Rebuild Icon Cache", and "Repair Icon Images" in the Tools menu.
3 - Save any IP theme folders from the "C:\Program Files\Stardock\Object Desktop\IconPackager\Themes" folder to a temporary folder.
4 - Uninstall IconPackager > reboot > remove any IconPackager folder left in "C:\Program Files\Stardock\Object Desktop" folder.
5 - Reset any file associations and file icon images manually, that may have been set to the default handling program included in Windows.
6 - Reinstall IconPackager 3 > reboot > test for functionality.
These are the general steps to reinstalling the older version, without going into the registry - which should not be necessary.
If you did not do steps #1 and #2 before uninstalling the newer version, you may want to reinstall it > apply a package > run the steps listed.
I know that IconPackager will restore the ".doc" icon to "Wordpad" document icon - probably due to Windows XP including the Wordpad program with the OS - so this may occur with any other associations where a program included with Windows will be reset to the default handler.
I am not a coder, so I have no competent explanation of where the 'restore' function looks to set associations.