Without confusing the issue I have just shut down the 777-200 Cleared for takeoff (KSEA) default completely cold including fuel isolators OFF. Saved the flight then taken a look at the *.flt file - the mixtures are as above in my post:

MixtureLeverPct=0.99615478515625

At no time has my (B777) system saved the mixture as:

MixtureLeverPct=0.0

So Mark your last statement could well be correct BUT your saying that when you save cold and dark with isolators OFF your mixtures are saved as zero?  :-/