You made me curious and look into the ezcsvimport script. Would it be possible to get a few rows from that export you have, say for 5 users? You could change names and e-mail addresses of course if you do not want me to look at any private data. I'd love to try and see if I can get the import to work, see if I run into your problem or not with the users not being visible in the admin.
Regards Robin
Board member, eZ Publish Community Project Board - Member of the share.ez.no team - Key values: Openness and Innovation.