The red/white star that indicates a new message only shows up on my "Messages" icon and not on my e-mail icon for Gmail. I have tested "Seperate" and "Theme Controlled" for "SMS and Email Inboxes" and have the same result. The new message appears in both boxes, but the new message star indicator only shows up on the "Messages" icon.
That is very close to the issue I'm experiencing, except that it is not a custom icon; it is the standard e-mail icon. It worked fine when I had OS 4.3, but then I upgraded to 4.5 (although it is not officially out for Alltel yet). I realize that it is possible that it is an OS issue, but I was really hoping to fix it on 4.5.