Hello,
there are still 2 things I do not yet understand - there are two users, user 1 facing the issue, for user 2 all is working:
1. When creating a similar lead with a user 2, and adding the prospect - is the organization then determined? Are you able to edit that lead with the affected user 1?
2. Is user 1 able to manually assign the organizational data in the lead?
Answering those questions may help further.
regards,
Johannes