Alter doesn't show in processlist
It sounds like the user that's executing the ALTER TABLE and the user who's running SHOW PROCESSLIST are not the same user, and the second user lacks the PROCESS privilege.

If you have the PROCESS privilege, you can see all threads. Otherwise, you can see only your own threads (that is, threads associated with the MySQL account that you are using).
— http://dev.mysql.com/doc/refman/5.6/en/show-processlist.html