banned_users.cfg will contain all of your perma-bans. ULX's bans.txt will grab the contents of banned_users.cfg and populate the bans.txt file with them. Thats the way it is supposed to work, so thats not a problem.
As for the !menu listing the bans as 'unknown' that is because a name wasn't included in the ban information in ULX's bans.txt. Which is fine, a name is irrelevant. All you need is a steamid and a ban duration.
Could you post the contents of your cfg/banned_users.cfg and your data/ulx/bans.txt? It might be something in the file that is causing a known issue.