I have a drupal 6 site. Recently I've set up a CDN (not using the module. manually, and more specifically Google PageSpeed Service) to serve my content which is cached by boost. What I've noticed that when cron is run, the boost cache files are not deleted. This happens probably because my real domain name - www.example.com points to the cdn, which internally uses a different cname to reach my server (origin.example.com). Unlike other CDNs, PageSpeed doesn't request pages from my server using the internal cname, but rather uses www.example.com.
So anyway, to make a long story short: when cron runs, it clears origin.example.com cache files and not www.example.com (and these are the files my visitors get). I should say also that this CDN doesn't support https, so I access the admin using origin.example.com.
So, any ideas....