I just had this happen to my games, so I looked into it and found the problem. I'm not sure what exactly causes it, but what happens is all the food items lose their morale modifiers - if you look at the food item it will say +0 morale (as your screenshot shows). The way the morale script determines that you have no food is that you have 0 morale bonus, so 0 morale bonus food does not count as food in morale terms (so you'll get a whopping -30 on top of the missing bonus).
Heres a fix for it.
...
This bug still hasn't been fixed, it's still there in 1.010.
Edit:
And I have no idea where to paste your fix into, since the numbers look different than the ones in 1.003.I guess I've found it...
44 1650 2 1224979098644774912 648518346341351424 2133 2 1224979098644774913 0 6 3 1224979098644774914 1 1224979098644774912 1652 3 1224979098644774915 648518346341351424 1224979098644774914 4 0 1507 1 1224979098644774915 2105 2 1224979098644774913 1 5 0 1653 3 1224979098644774916 648518346341351424 1224979098644774914 2105 2 1224979098644774913 1224979098644774916 3 0 3 0 2133 2 144115188075856313 1224979098644774913 2170 3 1224979098644774917 1369094286720630785 360287970189639680 2122 3 144115188075856314 1224979098644774917 30 2133 2 1224979098644774918 144115188075856314 2106 2 1224979098644774918 144115188075856313 2105 2 1224979098644774918 50 2133 2 144115188075856315 0 6 3 1224979098644774919 288230376151711814 288230376151711826 1 3 936748722493063328 1224979098644774919 41 527 3 1224979098644774920 1224979098644774919 1 2105 2 144115188075856315 1224979098644774920 3 0 2105 2 1224979098644774918 144115188075856315 4 0 31 2 144115188075856315 0 2133 2 144115188075856316 30 2106 2 1224979098644774918 144115188075856316 5 0 2133 2 144115188075856316 0 3 0 2133 2 144115188075856317 0 4 0 32 2 144115188075856031 0 1 1 936748722493063285 2133 2 1224979098644774921 72057594037927936 2122 3 144115188075856317 144115188075856031 10 2108 2 144115188075856317 1224979098644774921 2112 3 144115188075856317 1 31 2106 2 1224979098644774918 144115188075856317 3 0 2112 3 1224979098644774918 0 100 2133 2 72057594037927936 1224979098644774918
Edit: Gah! If I paste your fix there, the recent events morale value becomes negative.
It seems that your fix doesn't work with 1.010. The negative recent events morale value turns to positive in time after you won a few battles. For some reason, I keep getting negative recent events morale value. Obviously there's a problem.

Edit: In my game in 1.010, all the food items have lost their morale modifiers and not just that, the game thinks that I have no food even though I have plenty and gives me an additional
-30 morale for having no food!




