Hi Matt,
as soon as you get the console the first time, all bets are off. Consider the code to be "out of sync" and various things are not going to work anymore...
To really help reproduce the crash, we usually solicit certain .txt files - you can read up on that in the included documentation (bug report guide). Otherwise it is near impossible to recreate the cause, there are simply too many factors.
Once you get the console, close it, then bump your mouse on the right edge of the screen and click the "bolt" symbol to reboot the gizmo scripts. Then you can continue your flight. Only caveat: If you started the whole thing in "turn-around" or "cold and dark" then this will be the state after reboot. But you can work around that by clicking the option "ready to fly" before you reboot gizmo.
Good luck, Jan