I have a similar bug for power. My minmus base is powered via nuclear reactor, has a surplus of fuel and the overall consumption is less than the production, hence no change of running out. While in loaded it is like said, if unloaded after some time warp my power storage is signaled empty. Loading the vessel, my power is at 11K ec (max amount).
But that would be okay, but my food is running out too. I have my bases set up to be self sufficient, yet while unloaded the expiration time of food is decreasing one minute every second, which can't be.
A second vessel has the same problem, while in loaded my food reserves increase, while unloaded they diminish like nobody's business.
Anyone familiar with the food prob?