Certificates in the LAN settings? Maybe you mean proxy settings? That would make more sense with programs no longer working, since this affect most products using IE's settings. If it was the case, were the fields empty before you had them changed? If not do you remember what was there?

If you changed your certificates, unless you told it to block the certificates it will just ask you to trust the new ones as they find them and warn you that it's not in your trusted certificates.