Every transport will have different jitter characteristics, and typically fairly high jitter. This is the difference you are hearing. For transports, only output jitter matters, nothing else. You can lower this a bit by putting various treatments on the disk, but the simple and more effective method is to add a Synchro-Mesh reclocker in the S/PDIF cable. This has several advantages:
1) lowers the jitter to ~20psec - only the most expensive transports achieve this
2) upsamples the data to 24/96 - this forces the DAC to select a better sounding digital filter internally further improving SQ
3) provides galvanic isolation - breaks the ground-loop between the transport and the DAC which lowers the noise floor
4) it is no longer necessary to treat the disks to lower jitter
Here are measurements showing the effect of the Synchro-Mesh on an Oppo transport:
http://www.audiocircle.com/index.php?topic=154408.0
It is highly recommended that you use the best S/PDIF digital cable you can afford for the output to the DAC from the Synchro-Mesh. The Empirical Audio Standard BNC cable is $275 and will satisfy this requirement.
Here are some jitter plots showing how much jitter is added by typical S/PDIF coax cables:
http://www.audiocircle.com/index.php?topic=154425.0
Steve N.
Empirical Audio
Jitter is our expertise.