Slow INSERT/UPDATE on InnoDB
As you can see, the process that takes most time is "query end". There is an interlocking problem when multiple threads want to write the file at the same time, this way the log will be flushed every second: 

innodb_flush_log_at_trx_commit = 0

in the /etc/my.cnf file

Also, you should try Optimize InnoDB as explained above for future query improvement.