I am having a similar problem on about 4 sites. For some reason, WP Super Cache refuses to preload the home / front page. If I navigate to the homepage a cache file is generated, but that file disappears shortly after and doesn’t remain with the rest of the preloaded cache files.
If I switch the front page setting to a different page, then that new page won’t preload and the original home page will successfully preload. It’s like the plugin when querying the pages to preload ignores the root /.
What is also strange is that this problem is happening on 4 different websites. None of them will preload the home.
I don’t really understand permalinks and htaccess files all the well, but I’m wondering if there is a misconfiguration there.
Final thought is that 3 of this sites are hosted on Media temple… the last site was originally on mediatemple and was then migrated to a different server. All of the sites were set up using Media Temple’s one-click install… I’m wondering if there is a config error introduced through that process.
Help… I’m at a loss to what is causing this and how to fix it.