The normal steps would be:
1 - Start IconPackager > Tools menu > Restore all Icons > click "Yes" to confirm > click "Yes" button at the bottom of IconPackager dialog to apply.
2 - If step #1 did not work for Vista, I would suggest trying the system restore function in Vista (Start > Contol Panel > System and Maintenance > Backup and Restore Center > click the "Use System Restore to fix problems and undo changes to Windows" link > select a point before installing IconPackager to restore to > follow prompts to restore).
Hopefully, one of those will do it. If not, you will need to repair Windows using the install disc, which you will want to study via the Microsoft site before attempting. 