I wouldn't rule out the existence of seperate
codes. My Onkyo 939 is the same way with a
video source up and down only on the remote. I
have a cheapo universal Sony remote and using
it's supplied Onkyo receiver code, it gives direct access to video1, 2, and 3. So using the Sony's
IR signals and the up increments on the Onkyo
remote I can write macros for all video inputs
from 1 through 7 via the Pronto.

Also Oneforall has 'extended function codes'
for some components, but their e-mail support is
horrendous.