While continuing the Drupal Experiment and trying out various nice themes, I ran into a bit of a problem with some themes appearing for an instant in a very basic and unstyled format before the CSS kicks in and lays out the page the way it's meant to be shown.
After some trial and error, these problems manifested itself across various themes and across various theme engines in Drupal, so the initial suspicion that PHPTemplate might be at fault proved to be wrong.