It looks like there may be a bug in the Email Archive Agent that prevents it from storing metadata or setting a template when the email subject is null.
I looked at a few of my imports that were missing the templates and all fields and traced them back to some emails with no subject.
The archive agent event logs show a null reference exception, which is preventing the field assignments but not the import.
Because there is a real possibility of a NULL value in a subject line, it seems like there should be a check for that so it doesn't affect the other fields.
At the very least, an error like that should prevent the import since it would come in without metadata and if the profile is set to delete you could lose information.