I noticed today that one of my sites returned 403 Access denied on various pages with URLs like format/<foo>, although it was an alias for a taxonomy/term/<tid> taxonomy path which was actually available when not aliased. What could be going on ?

It turned out that this issue is caused by the http://drupal.org/node/28776 patch introduced in DRUPAL-6-7 to protect various VCS paths.

That patch introduced by this issue modifies the FilesMatch clause to match on ^format$ (for SVN), which causes any path containing the format string to be denied, causing that problem. Which gives the solution if this is a problem for you: either modify the relavant FilesMatch clause or rename every path containing format on your site.

Note that this specific subpattern has been rolled back and reworked after http://drupal.org/node/581706 for DRUPAL-7-0-ALPHA2, so Drupal 7 does not have this problem.