1. If you can reach the original developer, may be worth it to call him to figure out how he/she did it, so you can go in to fix it.
2. I found the theme's home page: http://store.informationarchitects.net/product/ia%C2%B3-template , although, they seem very clear they won't help.
3. My gut is telling me, perhaps, that whomever developed the site took this theme then hard-coded the navigation section in (John's #4 idea from above), since the theme's demo site only has three, the admin only has three options and apparently the options aren't changing anything (suggesting to me that whatever the options controlled was taken out).
I would search the code in the http://solutionssf.org/wp-content/themes/iA3%201.2 folder for the header and see if I could verify how that header was being constructed, if it was hard-coded or what.
[Sorry, too, for the delay! Gmail thought the notifications from the forum were spam...]