Appreciate the info, Dennis. I tried it out and actually ran into the same problem with the links that I had with vBindex, which led me to believe the problem lie in the main board settings, or the way they worked with the add-ons. Fortunately, the support for vBadvanced is much more comprehensive and responsive than that for vBindex, and although I didn't find a specific solution in their dedicated forums, I found some clues that eventually led me to the answer.
For posterity, I post what I found here in the hopes that it can help someone in the future. To summarize, instead of proper links in the nav bars of the portal pages (e.g.
http://www.yoursite.com/login.php), I was instead getting links that had the index page also incorrectly referenced (
http://www.yoursite.com/index.php/login.php). Obviously, this made many things not work correctly. The setting I had incorrect was AdminCP -> vBulletin Options -> Site Name / URL / Contact Details - > Forum URL. I had
http://www.yoursite.com/login.php listed, when the correct setting instead was
http://www.yoursite.com (no trailing '/'). You may or may not also need to change the 'Homepage URL' setting as well. I think that this issue came up in large part because I chose to install my board in the root of my hosting account, rather than making a sub-directory for it. I would recommend that others also put the forums in a sub-folder, just to avoid problems like this.
Haven't decided between vBindex or vBa at this time, still deciding which I prefer. Leaning towards the feature set in vBindex, but am a bit gunshy due to the lack of responsiveness here toward install issues.