I get its more of a building issue, but when posting in the building section, you get no replies.
However, scripters, usually have to do their own building as well and come across issues like this.
Maybe there are multiple welds there that are being activated and deactivated somehow which I have experienced before.
I would :BreakJoints() and retry, maybe experiment with :GetConnectedParts(). You can also visualize welds in the model tab of studio mext to constraints I believe.
Even though this is not a Roblox character, its just a mesh, with bones, what you posted started me to think, maybe the bone structure is causing issues, when you weld to a rig that was imported, and it has a InitialPoses folder, the weld will align the part to its value in InitialPoses folder.
So, learned something new, thanks for the help.
(oh, and to solve it, I just had to look up the entry for the Leaves_Head_Mesh, in InitialPoses, and remove the 180Y rotation in the cframes there)