I am surprised you can notice the difference between USB ports, especially considering you are applying digital volume control which means you are dithering down the original source signal... What are you using as a reference? Guess, I really have to start experimenting with my photo printer to see which USB ports gives better prints?
Not just me has noticed the differences of USB ports, some of my friends who use computer audio found the same.
As the name USB implies, it is SERIAL, both inside and outside the computer, the first port in the queue has the shortest distance to the processing center. The difference is rather obvious on my 6 years old IBM T60 laptop, it is due to another factor, the unequal oxidized levels of the metal surface, the disparity is less noticeable on my new ASUS laptop.
Regarding to data transferring rate, individual USB port on my MacBook can vary from constant 60m/s to constant 80m/s copying the same thing. The ports seem to have directions, some good at data in, some good at data out.
The gears I am using:
i7 ASUS laptop, Win8.1(OS setting optimized), foobar/HQplayer/Jplay/JRiver
---> Supra USB cable/ Vertere D Fi USB cable/ some other printer USB cables
---> Ciunas DAC
--->Cardas Golden Reference RCA interconnect cable
--->Sim Audio Moon W5.3RS power amp + handmade Supra conductor wire power cable
--->Bi-wire speaker cable.
Bass: Supra PLY 3.4,
High-Mid: brandless cable
--->B&W Matrix 801SE