A USERNAME is unique to each instance of DNN, not to each portal within the same DNN instance.  The DB table USERPORTALS defines what portal(s) each user account is linked to.

This arrangement has advantages and disadvantages.  On the "plus" side, if you have related portals you can allow users to "link" a single account (USERNAME) across those portals by re-registering on each portal with the same USERNAME and PASSWORD.  Any change to the user's account on one portal will be reflected on all portals (as you've already discovered) because it is actually the same account.

On the "minus" side, if you want one DNN instance to host independant sites that have no relation to each other, you cannot have the same USERNAME on different portals represent different (independant) accounts.  For DNN instances with large numbers of registered users, this can result in a lot of "Username 'johnsmith' already exsits" type messages when new users try to create accounts.

-mamlin