I’m not sure what I can do to help you on this one…but first, please confirm the following:
you installed two WordPress scripts in two different locations?
you installed the css classes plugin on both?
I am assuming you followed the setup tutorials correctly for Preference in relation to this plugin and widget styling?
Also, was it not possible for you to have one WordPRess install only where the member only areas are available only to members? Sounds a bit complicated for your setup…was there a reason using aMember? If you disable amember, does the classes work?