Woooow... After lots of researches, I figured out the problem.
Instead of calling "login.aspx" the first time into safari (in order to create the webapp), I must call index.aspx which redirect me to the login page because I'm not logged.
Using this, the behavior of my webapp is normal (I cannot explain why...) and the cache manifest REALLY cache the webapp.
I can access offline and online.
I hope this helps someone else with the same problem... (iOS mystery)