Generic answer, I suspect it's not related to the Apogee output, its related to receiver input.
- Try another optical cable
- Blow the dust out of the sockets
- can you do coax instead of optical?
- does it work at 16/44, but not 24/96?
- some devices don't play well together... for instance, that's why V3 has chip updates, so it will play with newer recorders. Hopefully you don't have incompatible hardware. My Onkyo surround receiver will play great with my iRiver, but not with my R09.
Good luck.