Just found a bug while creating the tutorial video...
It only happens when you create a new sprite collection, commit, and then create a sprite in the scene, and commit again (without closing down the editor). To fix it, add the following line in tk2dSpriteCollectionEditorPopup.cs, line 392:
spriteCollectionProxy.CopyToTarget();
tk2dSpriteCollectionBuilder.Rebuild(_spriteCollection);
spriteCollectionProxy.CopyFromSource();
It only occurs when doing this in particular, so any existing sprite collections will just work as normal. I clearly spent far too long testing various existing files for potential upgrade problems, and not the most obvious thing!
I'll release an update shortly that fixes it. In the mean time, please update the line above to fix the issue.