Hmm. We know that the output and the physical cable from the Direct TV box are both good. They worked fine when plugged into Optical 2. But, they don't work when plugged into Optical 1. So, something is likely the matter on the receiver side, either with the physical input for Optical 1 or in how V3 is configured.
So, next step: swap the other ends of the cables at the devices themselves. Take the cable now attached to the TV and connect it to the Direct TV box and move the cable from the Direct TV box to the TV. We know that one of the optical cables is good. This will tell us whether the other one is OK. If it is, you will once again hear audio from DIrect TV on V1, CD, and DVD.