Have you tried selecting the B-17 directly from the Free Flight screen? Load it up via that method, then shut the engines off if they are running. Do an overhaul in the hangar (Shift+7) just to be certain you have a mechanically sound airplane. Check the fluids in the payload manager (Shift+4, I think) to be sure you're all topped off. Hit the Cold Start button in the Pilot's notes menu (Shift+2) so the systems are completely shut down. Now, save your mission just like this using either the menu bar (hit ALT key) or just the semi-colon key ( ; ). You don't have to make your B-17G the default flight if you don't want to.
Now exit the flight and go back to the Free Flight menu. Choose the Load button and then select your newly saved mission. Your plane should be fully shut down but in excellent condition; you might want to check the fluids and oxygen though. Start the aircraft however you wish, either manually or with the CNTRL+E for autostart.
I won't guarantee this will fix your problem, but I start all of my flights as cold and dark (even default aircraft) and I haven't yet had a problem like you've described.
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