That’s a strange one. I’ve seen similar issues with imports before where the core data moves over fine, but the metadata or link tables for permissions don’t seem to 'hook' correctly in the new environment.
Have you checked if the Group IDs in your export file actually match the IDs in the new instance? Sometimes if the groups aren't created in the exact same order or if they have different internal IDs, the permissions end up pointing to nothing. It might also be worth doing a quick check of the logs during the import to see if there are any 'foreign key' or 'unauthorized' errors popping up silently.