Ok I think I figured out when the time system glitch happens, though I might be wrong. During my current run when the in game date went from December 31 to January 1, the hunger and thirst meter would not increase when I moved from nogas to shine town. This did not happen for saves that took place earlier in game. So I think the time system glitch occurs when you enter into a new year in game. I initially attributed it to the bounty hunter system because I always left the bounty grinding to the end which is around the time the game would 'change' into a new year. I don't know if this is what is actually going on but I hope that it might help narrow down the problem to specific code.