In case anyone else has this issue, I figured it out. There is a separate Logo setting for e-mail headers. I was thinking it was sharing the same header as the forum theme -- this is not the case.
Found this in General > Settings > E-mail Settings when looking for something unrelated. 😄 I believe the behavior is it pulls in the first logo you upload and keeps that setting, as when I changed the forum theme to a smaller logo, the large email header remained. Then I uploaded the smaller logo here. Just make sure to hit Save!
Now a normal size!!