The Yun has no real time clock. When it starts up, it makes an NTP request over the Internet to get the proper date and time. That can't happen if there is no internet connection, so it makes its best guess - which is certainly bound to be wrong. You've added an extra call to make another NTP request during startup, but that still requires an Internet connection, so it will also fail. As you discovered, your added NTP call accomplishes nothing - if you have an Internet connection, it's redundant; if you have no connection it still doesn't work.
If it's critical that you always have the correct date and time when you start up, then you will need to add some sort the f real time clock: either a battery backed up chip, a GPS receiver, cellular kink, or something similar.