This is not true, the changes were NOT made for SQ purposes at all. Here is the full story on the technical side of this, do with it as you will.
Quite a while ago while working on the opticalRendu I noticed the switch chip (the same switch chip was being used at that time) the connection to the CPU was going up and down, many times. I could not figure out what it was. Then an errata sheet came out for the switch chip which talked about the EEE bug, I wrote the code for the workaround on the main processor and fed that to the switch chip, It worked.
The EtherREGEN uses the same chip as I had originally on the oR (I picked it for the ER, but used it for prototyping on the oR since I knew it well). At this point the ER did not exist in the final form, it was several different boards trying out different parts of the system. I had not seen the EEE problem at all, probably because I was not testing it with anything that supported EEE. After I finally got the functionality for the ER working and I had the whole system up and running I wrote the code to send the workaround to the switch chip, it was much more complicated because I had to do it for 4 ports instead of one, it was also written for a completely different processor and environment. Somewhere along the line I made a mistake in that code that didn't actually implement the workaround, but I didn't know that at the time. Since I couldn't make the EEE problem happen, (it only happens for some boards and some equipment), I didn't know it wasn't working. Neither my testing, nor Alex's or the beta testers have the problem.
The problem only showed up when the ER went out into the field with enough different configurations that some people started having the problem. Remember that at this point I thought I had the workaround for the EEE stuff in every ER out there. It took some time and a lot of looking at the code to realize there was a bug in the code. While in the process I found a new errata sheet for the switch chip that added some new problems for the chip and workarounds for them.
At this point I fixed the EEE workaround code and found out that that it actually CAUSED dropouts every time an RJ45 A port connected. The connection would go up, then down, then back up. I could not figure this out, it didn't make any sense. I then tried adding the workarounds for the other two errata issues, both of which were supposedly only for rare "corner cases" which should only occur for long cables. One was for transmit, it increased the transmit amplitude very slightly, and the other was for receive which increased the probability of receiving very weak signals. Viola! The up down up behavior went away. I listened to it for quite some time with no problems, but did notice a small improvement in SQ, I still have no idea why.
Well that is it. This was all done in an attempt to improve connectivity issues. The sound change was not something that was intended, it was not something that was "tuned" it just showed up as a result of adding the workarounds for problems that already existed in the chip. I still have no idea how these changes could be affecting SQ.
John S.