It seems CTD occurs by day when FSDT automaticaly changes shadows setting when it is set in Fsx.cfg at FSX launch (so changing the setting manually after FSX starts has no effect on CTD).
It occurs on YOUR system!! I made all the possible tests, and there's are no issues whatsoever with the automatic enabling/disabling of the airplane shadows the Addon Manager does like ANY other FSDT scenery. I don't have any crashes, regardless if the shadows were enabled or not in the FSX.CFG
Note that, the FSX.CFG itself is not touched by the Addon Manager. It will be FSX *itself* that will update it to the current settings, when you exit from FSX.
The only difference is, I'm using FSX:SE, while you use Acceleration. We are not aware if there were issues or bugs or limitations in FSX Acceleration related to the handling of shadows that has been fixed by FSX:SE, but maybe this is the case. We have another system with FSX SP2 that we can try.