By any chance, might that 2nd item be a skeleton part? If so, that's the expected behavior; skeleton's always pop to the top of the tree, above regular models. If you didn't mean for that part to be a skeleton, you could create a new part, using the skeleton as a template instead of the usual start part. Also note, that it's only the first skeleton in a model that actually is locked in the top position. (To use multiple skeletons, config.pro settings must include "multiple_skeletons_allowed yes".) Although additional skeletons will initially pop to the top, you can drag them farther down the tree if you want, so you can constrain to other parts. You can even delete that first skeleton after addition additional ones, if you don't really need it.
If that's not it, then I have no idea. You should provide more information. Is the item still listed in the tree, it's just hidden? (Layer issue?) Or is the new model actually being inserted higher up in the tree?
