The Unity assets we already had still present the same behaviour if we downgrade to Unity 4.6. Generating new assets from the source files (png, json and atlas.txt) directly with the new runtime, however, worked fine in both Unity 4.6 and the beta 5.
This started to smell of Unity serialization issues :whew: . Comparing the source code across runtime versions, and checking the contents of two SkeletonData.asset files built with the runtime we had and the new one, I found that the "atlasAsset" field has now been replaced with an array, "atlasAssets", and Unity doesn't like that very much.
It seems that when SkeletonDataAsset::GetSkeletonData is called on an object deserialized from an existing data file (built with a previous runtime), it finds that "atlasAssets" is null and initializes it to an empty array. The original value of "atlasAsset" gets lost in limbo, and then we get the "Atlas not set" errors and "missing region" warnings.
I made a hack to confirm this and added back "atlasAsset" to SkeletonDataAsset: if we find that the new array property is null but the old property is not, we initialize the array with one element (the old prop.). Apparently, this fixes the problem, but I'm not too convinced of having to preserve the old property in the class in addition to the new one for the sake of compatibility, so there might be a better option.
Still, this doesn't explain why if we reimport until everything's fine, save everything, close and reopen the project we find ourselves in the same situation. Well, apparently the asset itself is not saved again when you reimport. I made SkeletonDataAssetInspector:😃rawReimportButton() call EditorUtility.SetDirty(target) to test, and that seemed to take care of this other problem, too.
I haven't thoroughly tested all possibilities, so there may be side effects that I'm not taking into account, or even laying the ground for further bugs, but these are my two cents about what we've been experiencing so far.
PS: I've seen there's a new runtime update in the repository, but from what I've seen so far the parts of code I'm mentioning here remain unchanged.
