I've got a some more information on what is happening when I use a single scene file.  I'm still not exactly sure "why" it's doing what it's doing, but here's the process I'm using.  If it helps, this is also running on a 64-bit Windows Vista installation, with wxPython 2.8 installed.  I get the same results whether or not I select the option to use the Poser materials on import.

1.  Import the scene file, selecting "Group Figures as single meshes"
2.  Rename each 'body' object as noted in prior post

If I look in the material editor, I start out with 84 materials, with separate materials for Mike and Vicky, but each figure has the same material names.  For example:  2_SkinHead, 1_SkinFace, etc. 

3.  Select Mike, Load SkinVue, click Select and then Swap

At this point if I look in the material editor, if I click on Mike I now have 52 materials, with a Michael4_Body_E, Michael4_Limbs_E, etc with M4's maps, But now all the 2_SkinHead, 1_SkinFace, etc maps for Vicky are gone from Mike's materials list.

But if I click on Vicky, it displays 84 materials again (??), with all of the original 2_SkinHead, 1_SkinFace, etc, listed for both Mike and Vicky.

4.  Select Vicky, load SkinVue, click Select and then Swap. 

If I look in the material editor now, I still have 52 materials listed when I click on both Mike and Vicky.

If I select Mike, I have Mike_Body_E, etc, with Mike's maps.

If I select Vicky, I have Vicky_Body_E, etc ... with Mike's maps.

I can at this point go in and manually reload all of Vicky's maps if I must, but this is just strange. 

As an additional test, I tried loading the scene again and then went back and renamed the materials for each object before applying SkinVue so that I had an M2SkinHead_1, V2SkinHead_1, etc.   That appeared to do the trick, but is way too much effort to do on a regular basis.

Right now the best solution when loading two figures that share material names appears to be to load them in from separate poser scene files so they have their own imported materials list.