Question(s):
Are we talking about "selectable" in the track inputs or in the Edit > Preferences > Audio - Devices section.
If you are merely talking about the available TRACK inputs go to your Sonar Audio Devices Preferences and make sure all those channels are selected. If they are grayed out then yes... something else is going on in which case....
What Samplerate are you set to?
I know that the ADAT/Optical connector (and such connectors in general) only allow 4 channels at 96khz samplerate and the full 8 at 48khz samplerate. So even though you said SPDIF is what is borking out maybe you meant the ADAT connection.
Just a couple longshot guesses/suggestions. Check that stuff out and return with your answers. If you solve the issue also return and post the solution for other users.
Cheers!
Edit: And please check out Wookie's question. I will follow that up with "Did you install the drivers from the disc that came with the hardware or did you download the most updated driver version for Vista?"
The reason this is important is because you generally do NOT want to install drivers from included discs because they are almost ALWAYS outdated and Focusrite did indeed have some problems with their drivers quite a few years back (so Vista may have been affected). Check for the LATEST Vista drivers on the Focusrite website and make sure you actually have them installed (check the point/version number... if they match you are good... if not dowanload and install the most recent Vista drivers).