I'm having the same problem. The first couple of play attempts, I didn't have problems with happiness but I did have a problem with Companionship, but could not figure out how to get to work on time. Most recent plays I figured out how to go to work, but now the character is never happy.
Sorry for the late answer, missed the thread As the question was asked earier, I'll just paste the reply here: We are still in the process of balancing stuff so various tomfuckery still happens. At the time you see this reply we had a lot of the stuff fixed and it must be easier to stay healthy and happy for your PC. In next release there will be a list of recent thingies affected your stats so you will know why something happened. As more content added to the game it will also be easier to get to it, stay tuned and thanks for your input!