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(Copied from Steam forum: http://steamcommunity.com/app/254320/discussions/0/364042262882764134/)

The short:
To be safe (until v1.01+ releases): Please do not "RESTART" after a death, please choose the Main Menu option and then Play game to get your new universe data correct. The "RESET" option from the pause menu should work fine.

The longer:
I believe that if you die, and hit "restart" from the pause menu that comes up after your mission/game summary screen, the game data will be in an odd state. That menu item is old and calls old code. Reset is what is supposed to be there. As such, when you save the game on that new run, it won't save correctly.

I'm pushing an update soon (in a couple days, after QA) that will hopefully fix this. Sorry for the issue, and thanks to those that helped us find it!
This fix is live so hopefully this bug is gone! :)