In short, every time I read an email through another email client (such as Gmail's Web client) while my computer is off, and then Thunderbird boots up and fetches new email, those emails I read (and got marked as read) get ignored by the filters.
What I would expect to happen is: new email is seen by Thunderbird (even if read), new email is run through the filters.
So, I would love an option to ensure that all my filters consider any and all new emails, regardless of their read status.