Are you are using Outlook Express with Hotmail, and the GoodContacts replies are in a Hotmail inbox?
Instead of the standard POP3, Hotmail uses a proprietary protocol, and GoodContacts is unable to monitor the Hotmail inbox. To process the replies, select the GoodContacts replies in the Hotmail inbox and drag them to the Inbox in the Outlook Express Personal Folders. If you have a POP3 account in addition to Hotmail, you can avoid this in the future by using the POP3 address for the replies. You can still include the Hotmail address in the profile that you send to your contacts.