I've never used MSI afterburner but I've overclocked 1060's to +1500 mem clock (9500MHZ total) using the nvidia-settings tool from nvidia on linux.
Can you share how you did this with nvidia-settings? Did you use GUI or command line? Do you have examples of command line or xorg.conf file entries? I had limited luck with this in Linux. I assume you're using latest nvidia drivers or an older version?