Very slow Insert and update on 20 core 250 Gb RAM dedicated MYSQL 5.5 server on Ubuntu
EDIT: after reading threw it, I noticed that your limiting it to 16 threads?
"innodb_read_io_threads = 16"
your server has 20 cores of cpu, and therefor you will only use a very small amount of CPU, try adding more threads and report back if it makes any difference,other then that i can't think of any thing else!

it may be due to server load, the fact that you have 20 cores may be useless, if the program can't multithread, whats your specs and general overall server load? other then that, I can't really think of any thing else that may be causing this.