Being tired is a bad time to do things

So, the reason the PCM4202 sounded so different to the digital input is because.... I have wired left to right and right to left (or LRCLK may be inverted). Also I think the phono cable I was using was faulty as well.

Having replaced the cable, swapped the channels in SigmaStudio (which is nice!), and set the levels between the two to almost the same, the analogue and digital inputs sound pretty much similar to me. If anything I would say the digital input sounds a little more clinical. I guess that is partly down to the sound card I am using to generate the analogue audio from my laptop in the first place (a Xonar U7).