Sorry if I wasn't clear when I originally posted this.
I do a "continous" aircraft, which means that once I land, deboard, I save the "flight" as to that location. When I start up again (I always close down FSX between Flights), I load the previous flight (via the saved name) wait for it to completely load (15 seconds to initialize most times) then I go into the Aircraft select the same aircraft I am on (Usually a PDMG Boeing variant) and just change the flight # and push ok.
That will restart the initialization process. It is at this time that it has another high likelihood of Failing.
TO note though it does not always do this and I am trying to capture this issue in a video log, which is proving elusive when I have it recording.