Status shows InnoDB: 128 rollback segment(s) are active waiting for purge to start
only for refer 

in windows server mysql 5.6

The reason why a crash recovery is performed even after a "normal shutdown" is because windows service manager does not wait long enough before killing the service forcefully. 60 seconds might not be enough to flush all dirty pages to disk. 
 There's a MySQL feature request to improve that. https://bugs.mysql.com/bug.php?id=45547 

The question then is how to make mysqld shutdown quicker so the service manager doesn't timeout after 60 seconds of waiting . 
 Answer is : 

o) Set in my.ini a small value for this. innodb_max_dirty_pages_pct=10 # (default value is 75) 
 o) Manually run STOP SLAVE; before the shutdown. 

 o) Manually shutdown the mysqld using "mysqladmin shutdown -uroot -p" before rebooting server. Instead of using windows service stop command..