I've just had the same problem after manually aligning two chunks in Standard (2.0.1). The top half of the object (a ring) is a chunk, the bottom half of the ring is another chunk. They wouldn't align very well automatically (it was close but not great) so I finished aligning them manually as meshes. The [T] symbol was next to each chunk, and viewing aligned chunks together, the complete ring mesh looked great. When I merge the two chunks, the new 'merged' chunk just has both sides of the object in their original locations. The attached screenshots hopefully show the problem, similar to the original poster. The file "misalign.jpg" shows the cameras all together in concentric circles where there should be two camera circles above and two below.
Any suggestions are welcome!