Just upgraded to 1.0.8. The milking pens I had (1x brahmin lvl3, 1x molerat lvl2) were invisible, but the structure appeared after refreshing. What did not appear were the animals. I then selected the brahmin blueprint on the molerat plot, and the cow spawned correctly. I then used cf unlocklevel to force an upgrade to lvl2. The construction of the lvl2 hut started and finished, but the brahmin from lvl1 was gone. It seems to me that the new lvl2 and lvl3 versions of these plots do not spawn animals for some reason. edit: I also TCLed to look under the plot. Still no animals.