I've seen cases of where optical out from a transport to a source vary in resulting SQ. There's more components at play than we think. You've mentioned cables and I can see that happening (although personally I've not experienced "good" from "bad" optical cable...maybe I was just lucky). Another which I've seen is the the quality of the optical out. Maybe it was coincidence in this case but some I had seen different in intensity strengths between two devices which had corresponding difference in SQ.
One obscure (and may be limited to iOS and VentureCraft's Go-DAP 4.0) is the sampling output rather than the physical component itself. I wrote a little post about it back in 2012 about it. http://www.head-fi.org/t/533084/venturecraft-go-dap-gd-04-for-iphone-4/60#post_8340059. I asked VentureCraft about it and they think their choice of a fix upsampling to 48kHz to the optical out resulted in it sounding flat.
I ordered two exact same optical cable from sysconcept, one sounds fantastic the other all vocals seem on the verge of cracking with occasional voice cracks. Go figure!