Have you installed the freeform hack? If you have, when you start the game with it, you will have all the researched animals (panda, black panther, white bengal tiger), buildings and foliage. If you save the game and load it up again, you will have to research them.
Also, but this I noticed only for buildings, I downloaded the researchable buildings from Zoo Tek. (Reptile houses, noctarium, etc..) I noticed they (though not all the time) have to be researched everytime I load the game. So they dissappear from the menu when you close the game and load it again.
That's one of the things I recall. Though, have you installed any downloads between the times you were playing the same zoo?