Confused About Relative Sonic Impact of DAC VS. Transport

Your Jolida has not been revealing the true recording. It may be introducing noise or jitter, the result may sound like colourations.
Each S/PDIF cable will present the sonics differently by their design, build quality and materials used in the cable,  even cable length. The goal is to control jitter being passed from transport to DAC.

Footers and vibration control on both components also contribute to optimal SQ.


 

It seems like you are swapping the S/PDIF coax from transport to Synchromesh. Just for kicks, try replacing the Empirical coax with a quality cable and see how this affects sonics. 

@stuartk , a nice system. I agree that since you’re using the Synchromesh and Steve’s cable there shouldn't be any jitter issues. I mentioned it earlier, vibration control is important to the dac and the transport, either with footers or cones in combination with a platform. Some components respond well to mass loading. 
Power cords for digital devices have a tremendous influence on sonics. You should be auditioning different PC’s since they will impart their own sonic signature to the component. Shielded cables are preferred according to many designers.
My big question to you is, are you using a linear PS on the Synchromesh or the stock wall-wart?

And as stated by others, separate power to analogue and digital is recommended. It will help reduce the noise generated by digital devices that can contaminate the mains. I’m not sure if you’ve installed dedicated lines, but the digital sources should be on an isolated power strip or conditioner with filtering.

In my digital setup every time I swapped a PC or SPDIF cable there was a change to the SQ and timbre of the music.

@stuartk , yes, there is a benefit to isolating digital from analogue. Well done.

You probably know that wall-warts are an inferior power supply. They introduce noise into the signal path and have a greater chance of contaminating the power line and other components.
I asked about how you were powering the Synchromesh for two reasons. The first is due to the noise factor of the wall-wart. The main reason is performance. A linear PS will provide clean regulated power, thus improving performance. It may also improve the leanness coming from the transport. 
 Every time I have upgraded a wall-wart to an LPS, the result was increased SQ; eg, better dynamics, imaging, soundstaging. When you’re ready to upgrade, may I suggest a Swagman Labs LPS as a high quality affordable PS. I’m using an upgraded unit on my reclocker.

Changing to copper conductors in your cables is worth trying.
You’re making progress trying to improve the sound of your digital, but after all is said and done, your best move may be to try a different transport. For the CD format which is supposed to be dying, there are many new transports coming to market.