Its hard to say exactly without a lot of detail but it sounds like you’re having problems with MAPI permissions vs AD permissions on the Public Folder.
You should set the permissions on the PF using Outlook using an admin account and see if you can correct it that way. If you set it with exchange system manager it may present problems for the NT accounts. It’s been a while for me re the migration route. My advice is to research and test before you begin and then migrate everything as fast as possible.
Most problems with migrations of exchange 5.5 and NT domains come from continued mixed-mode interopability problems, not necessarily something that didn’t replicate properly. As long as you can keep backups of all the PF permissions, mailbox permissions and the directory, you’re fine. Just migrate best of some decent testing and if you have issues with a group not being created or not having permissions, just review your pre-migration permissions and fix it accordingly in win2003/exchange2003 native mode.