I'm a bit lost as to what you are actually trying to do, or why Barry (who I'd normally not challenge what he posts
) posted what he did. The Saffire Pro 40 can be either an interface *or* an outboard ADAT preamp. If you are trying the later, and it sounds like you are, then sure it should work to drive ADAT into a Avid Omni.
The issue many folks run into there is the Omni only has a total of 8 inputs no matter what you are physically using, but I guess you know that since you are configuring the IO settings for the Omni. For intial playing you might just try to have the Omni use all 8 inputs from the ADAT.
If you are just using the preamps in the Saffire you really don't need optical cables running both ways. I expect you will not hear any difference than clocking the Saffire from the Omni or the Omni from the Saffire, I'd just start with what is simpler-clock the Omni from the Saffire.
The next most common confusion is sample rates. Start with the session at 48 kHz. The "native" clock rate of ADAT--which is what you are doing. Great. But make sure the Saffire Pro is set to that clock rate as well (otherwise I expect it will likely automatically use S/MUX output on the TOSLINK port).
Make sure you have the TOSLINK optical ports set to ADAT (not S/PDIF) In on the Omni and set to ADAT (not S/PDIF) out on the Saffire Pro 40. This is the next most likely cause of problems.