The issue with logging into the wiki first lies in MediaWiki's cache as far as I can tell. I've seen this on a few boards that I've installed this hack -- it's not that you're not logged in (in most cases) it's that mediawiki is showing a cache of an unlogged in page. As soon as you click to another page or perform an action that requires authentication (editing, etc) the wiki usually starts showing your login status.
For the rifeforum.com/rifeforum.org use case, you
cannot achieve SSO using this hack across two different
domains. It's just how it works - the cookies are not readable across domains. You will need some sort of federated authorization token to achieve this (i.e. SAML tokens or OpenID). You can achieve it with subdomains (i.e. forum.rifeforums.com, wiki.rifeforums.com, etc) but I have not tested this use case and it may prove buggy.
Regarding the vBa CMPS use cases - while I've used this successfully on forums running vBa (see:
http://community.ingres.com) I cannot guarantee compatibility with
any other installed products. The permutations of hacks is exponential and there's no way I can reasonably test against everything out there =[
Peter Walker brings up a good point. In troubleshooting any web application your first course of action should be to clear your browser's cache and cookies (much like how restarting Windows solves 90% of your problems). If I'm asked for support my first question is always "did you clear your cache and cookies?" Also, try it on different browsers; the issues you're having could be related to a specific browser. IE, FireFox, Safari, Opera, and Chrome should always be used to test since they represent the lion's share of the market.