Unlike some other MTAs, qmail distinguishes between injected mail, new messages entered into the mail system, and relayed mail, which is delivered from somewhere else. The difference is that injected mail needs to have its headers cleaned up, while relayed mail doesn't. Configuring qmail to clean up injected mail isn't hard, but depending on your setup, there are several possible ways to handle it.
The new-inject package contains two programs: new-inject, which is a replacement for qmail-inject, and ofmipd (Old Fashioned Mail Injection Protocol Daemon), an SMTP daemon that includes the functions of new-inject. Although you can survive without new-inject, it's easy to install and I encourage you to use it.
The usual ways to inject local mail are to feed it to qmail-inject or sendmail. Both do the cleanup automatically. (The qmail version of sendmail is a small wrapper that runs qmail-inject.)
Because new-inject is almost completely upward compatible with qmail-inject, use it in place of qmail-inject:
# cd /var/qmail/bin # mv qmail-inject qmail-inject.old # ln new-inject qmail-inject
(I've saved the old qmail-inject as qmail-inject.old in case there turned out to be some application that needed exactly qmail-inject's features, but after a year, I have yet to need it.)
Some programs inject local mail by opening an SMTP connection to the loopback address 127.0.0.1. If you've installed an SMTP listener following the instructions ...