Last week a reader (thanks Vlatko) emailed me letting me know that I had two URL structures working on the blog. They were:
The same problem was happening on all posts and pages. For example, a post could be accessed via:
as well as:
This is not a good thing for SEO, because Google might get confused when deciding which is the canonical version. In fact when I went to run the diagnosis tool on Google Webmaster Central I found a bunch of duplicate title tags being reported (caused by the second URL version).
Some time later Vlatko emailed me again saying that he had found the problem: the WP Super Cache plugin. WordPress is supposed to handle the canonical URL issue automatically, but somehow once I activated the WP Super Cache plugin the index.php redirect stopped working. Vatko was having the same problem on his blog, so it might be a bug on WP Super Cache itself.
I also believe that not everyone will be affected by it. It probably has something to do with your server settings.
Either way, if you are currently using WP Super Cache I recommend that you test to see if the index.php redirect is working. Make sure to log out first, and then try to access yourblog.com/index.php. If you are not redirected to the homepage you are having the same problem.
I will email the author of the plugin about it, and if you have any insights please share them with a comment.