All the passwords in htpasswd are different because they're crypted with their user_id. They should be unique to the user.
Not quite sure why some passwords are not storing correctly. So this only happens for users that were imported with CB Juice? Do users who register through registration have appropriate access?
You can restart the sync for a user by clearing the cb_folderaccess column within _comprofiler database. Once they attempt to login it should resync their password. However, it's designed to resync anytime their password doesn't match that column so it should be working fine as is.
Is your server Linux or Windows? Joomla version? CB version? CBSubs version?