Content Boxes not aligning

That’s probably a style issue. There’s no “one-size-fits-all” when it comes to CSS. I’ve tried to get it to be “one-size-fits-most” though.

The plugin offers several stylesheets with the download. However, and although most of the time these get used as-is, it is intended that you either work from one of those to customize, or better yet, create something totally integrated with your theme.

Here’s some info on creating/loading a custom stylesheet:
http://rocketgeek.com/tips-and-tricks/setting-up-a-custom-wp-members-stylesheet/

BTW… with the release of 2.8 (which is out in beta), there is going to be a new default style based on Twenty Twelve (which is the new WP default). But this will only install as the default in a new plugin install. Otherwise, it will remain whatever you had already set. There is also an easier dropdown to change through the pre-loaded styles in the plugin options.