I'm upgrading from v3.0.8 to 3.0.11
the Update File checker works pretty impressively well... except for 2 files. It stated that 'common.php' and 'index.php' were up to date and needed no changes.

This is untrue: common.php had a lot of code moved to the new include file includes\startup.php
Index.php is even worse: for my site I've renamed the original phpBB index.php file to forum_index.php and I created a new index.php file, So it's quite strange that the file checker didn't notice that