TextureEnder.jar is not converting some animations .txt files correctly into mcmeta. This isn't necessarily a bug with minecraft, but it is a big and necessary part of the 1.6 snapshots.
It seems that sometimes (notably long delays) timings are converted incorrectly. For example, this:
was converted into this:
Note how "time": 1 when it should be "time": 100. With this it obviously is easy for me to fix, but I have quite a few long and complex timings that get totally messed up.
This happened quite a few times with different textures and it didn't seem to be very consistent with any one timing in the txt file. Although each time I used the converter, the same files would be converted the same way.