From your original post, "Therefore, can anyone please advise or update the possiblities for using the DEQ 2496 and PC audio successfully?". I currently have set up a NAS 1 TB Drive, using a PC, Media Monkey with ASIO Drivers to access the music, then output via USB to Teralink 2 24bit/96kHz. From here using Toslink to DEQ2496 as a DAC, then to pre-amp onwards. The DEQ2496 previously was used as a step filter for the Magnepans as I felt they were too bright. However with the Dali Helicon 400, I remove the Step filter and use the DEQ purely as a DAC. Is this pure? If you look at Audio Physics and other active systems, Berhringer is used and later upgraded to DBX, Lyngdorf and other eq.
The cost of the DEQ is so cheap and the quality is so good, it is hard to move away from it.
If you consider the signal path, there are other areas that you could improve before upgrading from the DEQ.
I use balanced outputs for the whole system from the DEQ onwards. This really helps with the low level noise on all the components.
With regards to SPDIF outputs, toslink, BNC, etc, as an engineer, the Toslink should provide the purest transport - glass being the cleanest. Plastic will fade the optical light for longer distances and may mar the light with it less then crystalline properties. However cheap glass will have the same effect. It is not cheap or easy to make good glass optical fiber. Having many strands allows the light to have many redundant paths, hence improving the quality of the light that arrives. However if the glass is of high quality, then only 1 strand is all that is necessary. Although not of high quality, optical lines travel across the Atlantic and pacific (with repeaters every so often) but each signal runs only on one strand, not multiple. I used to be with the group that did this. Many forum posting prefer the "warmer" sound from BNC. I suspect it is because BNC has a capacitance and this will alter the sound - rounding off the highs, smoothing the noise and interference. BNC can carry very high frequencies - video, so my explanation could be wrong. It could also be that the BNC converters are changing the sound and not the cable itself.
For the ultimate PC music, store music as uncompress (WAV), use a very good USB cable, make sure the DAC's have a isolator, use Asynchronous USB, reclocking is best and isolating the PC ground which is really noisy works. After that you are home free.
Personally I have enjoyed the DEQ. It is not superb music, but up there and I have many other weaker links to correct before I change out the DEQ.
The USB hub got to go.