I can confirm this bug-- I've just encountered it myself and can't shake it.
SetSkeleton2DDepth has depth sorting issues, at least in regards to Spriter Pro. No matter how I try to put a Skeleton behind a sprite using SetSkeleton2DDepth I can't do it. So, my guess it's an issue with how AppGameKit is importing Spriter files? Unfortunate timing too, because I'm building a Ludum Dare game!
Other Spriter Pro import issues: If you use a sprite twice in Spriter Pro (such as using an eye twice) only one will be rendered in AppGameKit (or, it maybe puts both in the same location because it assumes they both belong to the same bone?), so I have to duplicate an image and call them eye1 and eye2 for them both to show in AGK.
Something that would also be nice, the ability to clone 2D Skeletons... so, we don't have to preload 20-30 skeletons and keep them in memory if not using them, we can just clone them as necessary.
~~ LillyByte ~~
http://www.dymoria.com