When upgrading the game to 0.11.0 alpha version in Desura the installation directory and/or start scripts don't always get updated properly. I'm not really sure what causes this or why it doesn't happen every time.
So if you see an error message complaining about file/directory access when trying to launch the game after upgrading to version 0.11.0 you are likely facing this same problem. Solution: Manually uninstalling the game from Desura and then re-installing it seems to fix the problem.
I'm sorry for the inconvenience. I will post here when/if I come up with a better solution to this problem.