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The "--system" switch should only affect the UID/GID assigned to the user object.
A specific UID and GID range is set aside for "system accounts" (in /etc/login.defs, I believe) and if you want to make the account a non-system account later, you'll have to change the UID of that account.
I'm able to log in interactively using a "system" account on my system as long as the account has a valid shell. The adduser script on your system may have set the shell to /bin/false or something similar. You can check this with getent passwd username.
It is also possible that a setting in PAM could prevent interactive logins for accounts with UIDs in the "system" range.