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Is there a reason why you're using SMD files?
If you're exporting/importing directly between Milkshape and SimPE, you can right-click the GMDC to export/import meshes, and import/export as "Sims 2 unimesh import (or exporter) v.4.09A" instead. This has the skeleton and bone assignments, morphs, etc. and works fine for CAS items and most furniture with joints.
There are a few items you'll get errors on, but that's usually more of a Milkshape issue (it has issues with some meshes with multiple morphs, and things like that - bedding is one of those things, but you can import and change the bed frame). Usually you can find workarounds for these items.
If you're using Blender or other programs in between, then I'm not sure...