In the email where you're not seeing the logo properly, if you choose to View Source, what is the HTML content of the message? That will give you information such as BASE HREF and the IMG tag that renders the image. If those are pointing to the wrong place, then naturally you're not going to see the image.
If you didn't use the same original name for the image, then I'm not surprised that it's not showing. The /email/header.jpg file is the name of the image that's expected.
A clean new uncustomized install of Zen Cart will build those correctly. So, unless you've altered your email templates in the /email/ folder or made other changes to your site either directly or via addons, then it should work fine.




