I'm on latest version (currently 0.96) using Steam.
When I create a new Draconian online region colony, every time I go back and load the save again, my resources are set to the initial values you get when you start a new game.
Didn't test it on offline colony and other races.
I also experienced this bug for both new draco and human regions so it is not dependent on race, as well as many other players in global chat.
The way to currently sidestep this bug is to play the game for a longer session in your first session. What solved it for me was to play the game continuously (without exiting) for 2.5-3 hours. Try it and let me know if it fixes yours.