Hello.
> Presumably you were running as root when you started that command.
Yes, this is true. Exim is started in rc.d scripts by root.
> Running Exim using -C has a number of complications. Do you get the same
> problem if you run Exim without using -C?
Removing -C argument (with copying 'configure' to exim's default etc folder)
does not give any effect.
> Try starting the daemon, then sending it a HUP signal, *then* sending
> the message.
Yes, this works - second line in header files changes to "mailnull 26 6".
I also tried to check how exim 4.54 fills header files just after restart
and found that it has similar behaviour. First time it uses "root 0 0",
but it switches to "mailnull 26 6" after HUP.