Hmm, that's odd.  I just tried a tried a test with a an M4 and V4 in the scene and it worked fine.  Are you sure that the names of the characters are different?  If you imported the scene as a single scene with two characters and then selected "Group Figures as single meshes", then in all likelihood, Vue assigned the same names to the characters (e.g. Body).  The name of each character you apply SkinVue to has to be unique, otherwise, it will load materials based on what's in memory versus loading materials from disk.  So here is a suggested workflow depending on if you import a scene containing multiple characters or import several scene files each with a single character:

Importing a single Poser file containing multiple characters:

1. Import the scene file
2. In the world browser, select the character (body) and rename it (e.g. V4).  Note: if you are using M4 with genitals, it will have two objects both named "body" - group the Character and Genitals objects together.
3. Select the first character, fire up SkinVue and swap
4. Select the second character, fire up SkinVue and swap

Importing Multiple Characters each in their own Poser file:

1. Import character 1
2. Fire up SkinVue and swap
3. Import character 2
4. Fire up SkinVue and swap