FTP uploads and file permissions using Transmit

Transmit has the capability to change the permissions of a file as it uploads it to your server. Make sure the check-box "Auto-set my permissions" is unchecked. Typically, Drupal (all versions) like to have most of their files at octal 755 or 775. If you accidentally have Transmit set to change things to 644 or something similar, your newly-uploaded Drupal site will not work.