It sounds as if your unit is bypassed. You don't mention the state of the bypass switch at all which suggests that you are maybe not considering this.
If this is not the case, set the unit up for relay bypass and see if you can hear the relays click when you hit the bypass switch. If you can, check your cabling. If not, there is probably a hardware fault.
SPDIF is always sent, regardless of the I/O settings. It has no bypass relay, so is unaffected by the bypass state.
V2.000 is very old software, even for this old machine, so will probably have numerous issues. Unfortunately, Eventide no longer supplies updates for the DSP4000.
