BlockAlyzer was developed to work on rather large pages with more complex setups. Anyway, there might be some issues I didn’t discover. Please use the forum on wordpress.org to ask for support.
BlockAlyzer perfectly works with Cache. Anyway, you should flush the cache once the plugin is installed or else the frontend code to measure adblock users wouldn’t be included.
Multilingual and Multisite
If you are running a multilingual WordPress Multisite (aka Network) chances are, the language BlockAlyzer gets from your blog is not the language your blog is written in. A similar problem occurs when you have a multilingual WordPress using a plugin like WPMU or qtranslate. There will soon be a solution for the first situation, but I am open for suggestions about the second one.
Problems and issues with other plugins.
CSS-JS-Booster: this plugin hasn’t been updated a very long time. Deactivate it or use another minify plugin that allows you to set exceptions (see Minify)