Broken: 2.76 f337fea and above
Short description of error
It seems that object transparency sorting is directly related to object creation order.
This behaviour makes impossible to correctly sort the objects transparency in linked dupligroups.
Even if a possible workaround is to manually delete in the source file all the meshes and recreate them in the desired order, this is not a handy way of dealing with very complex files with multiple dupligroups and links.
Exact steps for others to reproduce the error
Open the included scene.blend file and you'll see on the left a CubeMonkey geometry and on the right a MonkeyCube one.
They are both linked from the included source.blend file.
The CubeMonkey dupligroup has inside two meshes, a cube and a suzanne, with the cube, having a transparent material, created before the monkey.
The MonkeyCube dupligroup has inside a duplicate of those meshes, but the cube duplicate was created after the monkey one.
As you can see, transparency works only if the object with the transparent material is created first.