I'm sorry, I can't reproduce this issue. I used the settings you posted above, then sent G1 E1 first with x16 microstepping. Then I sent M350 to change the microstepping to 8, then 2, then 1 and repeated the G1 E1 command in each case. The motor moved the same amount every time, but was much noisier with lower microstepping.
I am using the candidate firmware build for 2.02RC4, but I don't think there have been any changes that would account for the problem going away. But I suggest you try upgrading to 2.02RC4 anyway when I release it.