
By default, your flight usually starts with Megis, which is central time(- 6 hrs. from GMT). This time also is set to your system time, no matter where you live. If you start a flight from a different time zone, it will reflect the time zones time, not the system time.
Example: Create a flight in megis and look at you time, it should be the same as your system time. Change the starting airport to denver and the time will move back one hour. It sounds confusing, but all aircraft times are referenced to GMT.
Hope this clarifies things a little.