Just to make it clear. OBJ groups are actually groups of FACES. In other words, the OBJ format doesn't group vertices but polygons.
When I added support for groups in Blender I used the vertex groups because that's what was available. Blender vertex groups were not exactly meant for that but it was the best thing available. So, yes, keep in mind that when you select/deselect parts of the model you should strictly operate in face selection mode.

Hope this helps.

Paolo

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